1
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Kaur R, Frederickson A, Wetmore SD. Elucidation of the catalytic mechanism of a single-metal dependent homing endonuclease using QM and QM/MM approaches: the case study of I- PpoI. Phys Chem Chem Phys 2024; 26:8919-8931. [PMID: 38426850 DOI: 10.1039/d3cp06201e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Homing endonucleases (HEs) are highly specific DNA cleaving enzymes, with I-PpoI having been suggested to use a single metal to accelerate phosphodiester bond cleavage. Although an I-PpoI mechanism has been proposed based on experimental structural data, no consensus has been reached regarding the roles of the metal or key active site amino acids. This study uses QM cluster and QM/MM calculations to provide atomic-level details of the I-PpoI catalytic mechanism. Minimal QM cluster and large-scale QM/MM models demonstrate that the experimentally-proposed pathway involving direct Mg2+ coordination to the substrate coupled with leaving group protonation through a metal-activated water is not feasible due to an inconducive I-PpoI active site alignment. Despite QM cluster models of varying size uncovering a pathway involving leaving group protonation by a metal-activated water, indirect (water-mediated) metal coordination to the substrate is required to afford this pathway, which renders this mechanism energetically infeasible. Instead, QM cluster models reveal that the preferred pathway involves direct Mg2+-O3' coordination to stabilize the charged substrate and assist leaving group departure, while H98 activates the water nucleophile. These calculations also underscore that both catalytic residues that directly interact with the substrate and secondary amino acids that position or stabilize these residues are required for efficient catalysis. QM/MM calculations on the solvated enzyme-DNA complex verify the preferred mechanism, which is fully consistent with experimental kinetic, structural, and mutational data. The fundamental understanding of the I-PpoI mechanism of action, gained from the present work can be used to further explore potential uses of this enzyme in biotechnology and medicine, and direct future computational investigations of other members of the understudied HE family.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
| | - Angela Frederickson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
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2
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Li B, Zhai G, Dong Y, Wang L, Ma P. Recent progress on the CRISPR/Cas system in optical biosensors. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:798-816. [PMID: 38259224 DOI: 10.1039/d3ay02147e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) protein systems are adaptive immune systems unique to archaea and bacteria, with the characteristics of targeted recognition and gene editing to resist the invasion of foreign nucleic acids. Biosensors combined with the CRISPR/Cas system and optical detection technology have attracted much attention in medical diagnoses, food safety, agricultural progress, and environmental monitoring owing to their good sensitivity, high selectivity, and fast detection efficiency. In this review, we introduce the mechanism of CRISPR/Cas systems and developments in this area, followed by summarizing recent progress on CRISPR/Cas system-based optical biosensors combined with colorimetric, fluorescence, electrochemiluminescence and surface-enhanced Raman scattering optical techniques in various fields. Finally, we discuss the challenges and future perspectives of CRISPR/Cas systems in optical biosensors.
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Affiliation(s)
- Bingqian Li
- School of Special Education and Rehabilitation, Binzhou Medical University, Yantai 264003, China.
| | - Guangyu Zhai
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Yaru Dong
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Lan Wang
- School of Special Education and Rehabilitation, Binzhou Medical University, Yantai 264003, China.
| | - Peng Ma
- School of Basic Medicine, Binzhou Medical University, Yantai 264003, China.
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3
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González Castro N, Bjelic J, Malhotra G, Huang C, Alsaffar SH. Comparison of the Feasibility, Efficiency, and Safety of Genome Editing Technologies. Int J Mol Sci 2021; 22:10355. [PMID: 34638696 PMCID: PMC8509008 DOI: 10.3390/ijms221910355] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 08/26/2021] [Accepted: 09/24/2021] [Indexed: 12/15/2022] Open
Abstract
Recent advances in programmable nucleases including meganucleases (MNs), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) have propelled genome editing from explorative research to clinical and industrial settings. Each technology, however, features distinct modes of action that unevenly impact their applicability across the entire genome and are often tested under significantly different conditions. While CRISPR-Cas is currently leading the field due to its versatility, quick adoption, and high degree of support, it is not without limitations. Currently, no technology can be regarded as ideal or even applicable to every case as the context dictates the best approach for genetic modification within a target organism. In this review, we implement a four-pillar framework (context, feasibility, efficiency, and safety) to assess the main genome editing platforms, as a basis for rational decision-making by an expanding base of users, regulators, and consumers. Beyond carefully considering their specific use case with the assessment framework proposed here, we urge stakeholders interested in genome editing to independently validate the parameters of their chosen platform prior to commitment. Furthermore, safety across all applications, particularly in clinical settings, is a paramount consideration and comprehensive off-target detection strategies should be incorporated within workflows to address this. Often neglected aspects such as immunogenicity and the inadvertent selection of mutants deficient for DNA repair pathways must also be considered.
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Affiliation(s)
- Nicolás González Castro
- School of Biosciences, Faculty of Science, University of Melbourne, Parkville 3052, Australia; (N.G.C.); (G.M.); (C.H.); (S.H.A.)
| | - Jan Bjelic
- School of Biosciences, Faculty of Science, University of Melbourne, Parkville 3052, Australia; (N.G.C.); (G.M.); (C.H.); (S.H.A.)
| | - Gunya Malhotra
- School of Biosciences, Faculty of Science, University of Melbourne, Parkville 3052, Australia; (N.G.C.); (G.M.); (C.H.); (S.H.A.)
| | - Cong Huang
- School of Biosciences, Faculty of Science, University of Melbourne, Parkville 3052, Australia; (N.G.C.); (G.M.); (C.H.); (S.H.A.)
| | - Salman Hasan Alsaffar
- School of Biosciences, Faculty of Science, University of Melbourne, Parkville 3052, Australia; (N.G.C.); (G.M.); (C.H.); (S.H.A.)
- Biotechnology Department, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Shuwaikh 13109, Kuwait
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4
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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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5
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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: 63] [Impact Index Per Article: 12.6] [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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6
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Understanding the indirect DNA read-out specificity of I-CreI Meganuclease. Sci Rep 2018; 8:10286. [PMID: 29980759 PMCID: PMC6035192 DOI: 10.1038/s41598-018-28599-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/26/2018] [Indexed: 11/19/2022] Open
Abstract
The high DNA specificity of homing endonucleases makes them a powerful protein scaffold to engineer enzymes for genome manipulation. Understanding their molecular recognition of DNA is an important prerequisite to generate engineered enzymes able to cleave DNA in specific desired genome sites. Protein-DNA recognition studies have been mostly focused on specific direct contacts between amino acid side chains and bases to redesign the binding interface. However, the important role of indirect readout in the central region of the target DNA of the homing endonuclease I-CreI suggested that indirect readout may play a key role in the redesign of protein-DNA interactions. The sequences of the I-CreI central substrate region, 2NN, along with the adjacent 5NNN, are key for substrate cleavage. Here, we analyse the mechanism of target discrimination at the 5NNN region by the I-CreI protein, revealing its critical role in the location and occupancy of the catalytic metal ions, which is crucial for cleavage. Our data highlight the importance of indirect readout for target DNA cleavage, thus aiding I-CreI engineering when targeting new DNA sequences.
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7
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Bilto IM, Guha TK, Wai A, Hausner G. Three new active members of the I-OnuI family of homing endonucleases. Can J Microbiol 2017; 63:671-681. [PMID: 28414922 DOI: 10.1139/cjm-2017-0067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In vitro characterization of 3 LAGLIDADG-type homing endonucleases (HEs) (I-CcaI, I-CcaII, and I-AstI) that belong to the I-OnuI family showed that they are functional HEs that cleave their respective cognate target sites. These endonucleases are encoded within group ID introns and appear to be orthologues that have inserted into 3 different mitochondrial genes: rns, rnl, and cox3. The endonuclease activity of I-CcaI was tested using various substrates, and its minimum DNA recognition sequence was estimated to be 26 nt. This set of HEs may provide some insight into how these types of mobile elements can migrate into new locations. This study provides additional endonucleases that can be added to the catalog of currently available HEs that may have various biotechnology applications.
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Affiliation(s)
- Iman M Bilto
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Tuhin K Guha
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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8
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Guha TK, Hausner G. Insertion of Group II Intron-Based Ribozyme Switches into Homing Endonuclease Genes. Methods Mol Biol 2017; 1498:135-152. [PMID: 27709573 DOI: 10.1007/978-1-4939-6472-7_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Fungal mitochondrial genomes act as "reservoirs" for homing endonucleases. These enzymes with their DNA site-specific cleavage activities are attractive tools for genome editing, targeted mutagenesis and gene therapy applications. Herein, we present strategies where homing endonuclease open reading frames (HEases ORFs) are interrupted with group II intron sequences. The ultimate goal is to achieve in vivo expression of HEases that can be regulated by manipulating the splicing efficiency of the HEase ORF-embedded group II introns. That addition of exogenous magnesium chloride (MgCl2) appears to stimulate splicing of nonnative group II introns in Escherichia coli and the addition of cobalt chloride (CoCl2) to the growth medium antagonizes the expression of HEase activity (i.e., splicing). Group II introns are potentially autocatalytic self-splicing elements and thus can be used as molecular switches that allow for temporal regulated HEase expression. This should be useful in precision genome engineering, mutagenesis, and minimizing off-target activities.
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Affiliation(s)
- Tuhin Kumar Guha
- Department of Microbiology, 401 University of Manitoba, Buller Building 213, Winnipeg, MB, Canada, R3T 2N2
| | - Georg Hausner
- Department of Microbiology, 401 University of Manitoba, Buller Building 213, Winnipeg, MB, Canada, R3T 2N2.
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9
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Fine EJ, Cradick TJ, Bao G. Strategies to Determine Off-Target Effects of Engineered Nucleases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [DOI: 10.1007/978-1-4939-3509-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Zhou H, Li P, Wu D, Ran T, Wang W, Xu D. EheA from Exiguobacterium sp. yc3 is a novel thermostable DNase belonging to HNH endonuclease superfamily. FEMS Microbiol Lett 2015; 362:fnv204. [PMID: 26500089 DOI: 10.1093/femsle/fnv204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2015] [Indexed: 11/12/2022] Open
Abstract
The HNH endonuclease superfamily usually contains a conserved HNH motif in the sequence, and the second subfamily of it uses N to replace the second H in the HNH motif. A bacterium with extracellular thermostable DNase was isolated and identified as Exiguobacterium sp. yc3. A 20 kDa putative DNase was later purified and the encoding gene of it was amplified and sequenced, the deduced amino acid sequence analysis showed that the protein belongs to the HNH endonuclease superfamily, and therefore it was named as EheA ( E: xiguobacterium H: NH E: ndonuclease). Characterization of the recombinant EheA confirmed that EheA is a DNase. By site-directed mutation method, H116, N141 and N156 were proved to be essential for the DNase activity. EheA is the first experimentally determined bacterial source endonuclease belonging to the second subfamily of HNH superfamily. Further bioinformatic analysis showed that EheA homologue genes are conserved in the Exiguobacterium species, which suggests their possible important functions for Exiguobacterium species. And as a thermostable DNase, EheA also has a promising future in many application fields.
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Affiliation(s)
- Hanying Zhou
- Key Laboratory of Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China, 210095
| | - Pengpeng Li
- Key Laboratory of Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China, 210095
| | - Dongxia Wu
- Key Laboratory of Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China, 210095
| | - Tingting Ran
- Key Laboratory of Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China, 210095
| | - Weiwu Wang
- Key Laboratory of Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China, 210095
| | - Dongqing Xu
- Key Laboratory of Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China, 210095
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11
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Molina R, Redondo P, López-Méndez B, Villate M, Merino N, Blanco FJ, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G. Crystal Structure of the Homing Endonuclease I-CvuI Provides a New Template for Genome Modification. J Biol Chem 2015; 290:28727-36. [PMID: 26363068 DOI: 10.1074/jbc.m115.678342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Indexed: 01/24/2023] Open
Abstract
Homing endonucleases recognize and generate a DNA double-strand break, which has been used to promote gene targeting. These enzymes recognize long DNA stretches; they are highly sequence-specific enzymes and display a very low frequency of cleavage even in complete genomes. Although a large number of homing endonucleases have been identified, the landscape of possible target sequences is still very limited to cover the complexity of the whole eukaryotic genome. Therefore, the finding and molecular analysis of homing endonucleases identified but not yet characterized may widen the landscape of possible target sequences. The previous characterization of protein-DNA interaction before the engineering of new homing endonucleases is essential for further enzyme modification. Here we report the crystal structure of I-CvuI in complex with its target DNA and with the target DNA of I-CreI, a homologue enzyme widely used in genome engineering. To characterize the enzyme cleavage mechanism, we have solved the I-CvuI DNA structures in the presence of non-catalytic (Ca(2+)) and catalytic ions (Mg(2+)). We have also analyzed the metal dependence of DNA cleavage using Mg(2+) ions at different concentrations ranging from non-cleavable to cleavable concentrations obtained from in vitro cleavage experiments. The structure of I-CvuI homing endonuclease expands the current repertoire for engineering custom specificities, both by itself as a new scaffold alone and in hybrid constructs with other related homing endonucleases or other DNA-binding protein templates.
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Affiliation(s)
- Rafael Molina
- From the Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, C/Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Pilar Redondo
- From the Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, C/Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Blanca López-Méndez
- the 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
| | - Maider Villate
- the Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia 800, 48160 Derio, Spain
| | - Nekane Merino
- the Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia 800, 48160 Derio, Spain
| | - Francisco J Blanco
- the Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia 800, 48160 Derio, Spain, IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, 48013 Bilbao, Spain, and
| | - Julien Valton
- CELLECTIS S. A., 8 rue de la croix Jarry, 75013 Paris, France
| | | | | | - Jesús Prieto
- From the Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, C/Melchor Fernández Almagro 3, 28029 Madrid, Spain,
| | - Guillermo Montoya
- From the Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, C/Melchor Fernández Almagro 3, 28029 Madrid, Spain, the 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,
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12
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Casini A, Storch M, Baldwin GS, Ellis T. Bricks and blueprints: methods and standards for DNA assembly. Nat Rev Mol Cell Biol 2015; 16:568-76. [DOI: 10.1038/nrm4014] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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13
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Molina R, Marcaida MJ, Redondo P, Marenchino M, Duchateau P, D'Abramo M, Montoya G, Prieto J. Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold. J Biol Chem 2015; 290:18534-44. [PMID: 26045557 DOI: 10.1074/jbc.m115.658666] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/27/2022] Open
Abstract
Homing endonucleases are useful tools for genome modification because of their capability to recognize and cleave specifically large DNA targets. These endonucleases generate a DNA double strand break that can be repaired by the DNA damage response machinery. The break can be repaired by homologous recombination, an error-free mechanism, or by non-homologous end joining, a process susceptible to introducing errors in the repaired sequence. The type of DNA cleavage might alter the balance between these two alternatives. The use of "nickases" producing a specific single strand break instead of a double strand break could be an approach to reduce the toxicity associated with non-homologous end joining by promoting the use of homologous recombination to repair the cleavage of a single DNA break. Taking advantage of the sequential DNA cleavage mechanism of I-DmoI LAGLIDADG homing endonuclease, we have developed a new variant that is able to cut preferentially the coding DNA strand, generating a nicked DNA target. Our structural and biochemical analysis shows that by decoupling the action of the catalytic residues acting on each strand we can inhibit one of them while keeping the other functional.
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Affiliation(s)
| | | | | | - Marco Marenchino
- NMR Unit, Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), c/Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | | | - Marco D'Abramo
- Department of Chemistry, University of Rome "La Sapienza," Piazzale Aldo Moro 5, 00185, Rome, Italy, and
| | - Guillermo Montoya
- From the Macromolecular Crystallography Group and Novo Nordisk Foundation Center for Protein Research, Protein Structure and Function Program, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jesús Prieto
- From the Macromolecular Crystallography Group and
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14
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Zhao G, Hu T, Li J, Wei H, Shang H, Guan Y. A RCA-based assay for analyzing individual strand break in DNA heteroduplex cleavage by restriction endonucleases. Chem Commun (Camb) 2015; 50:11930-3. [PMID: 25157639 DOI: 10.1039/c4cc05314a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We have developed a rapid and high-throughput assay based on rolling circle amplification, to distinguish individual strand cleavage of DNA duplexes by restriction endonucleases. As an illustration, we analyzed nicking activity of Nb.BbvCI and uneven cleavage of LNA modified DNA by EcoRI. This assay has potential for analyzing protein-DNA interactions.
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Affiliation(s)
- Guojie Zhao
- Key Laboratory of Medical Cell Biology (Ministry of Education), Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning 110001, China.
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15
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Maggio I, Gonçalves MAFV. Genome editing at the crossroads of delivery, specificity, and fidelity. Trends Biotechnol 2015; 33:280-91. [PMID: 25819765 DOI: 10.1016/j.tibtech.2015.02.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/26/2015] [Accepted: 02/27/2015] [Indexed: 12/26/2022]
Abstract
Genome editing (GE) entails the modification of specific genomic sequences in living cells for the purpose of determining, changing, or expanding their function(s). Typically, GE occurs after delivering sequence-specific designer nucleases (e.g., ZFNs, TALENs, and CRISPR/Cas9) and donor DNA constructs into target cells. These designer nucleases can generate gene knockouts or gene knock-ins when applied alone or in combination with donor DNA templates, respectively. We review progress in this field, with an emphasis on designer nuclease and donor template delivery into mammalian target cell populations. We also discuss the impact that incremental improvements to these tools are having on the specificity and fidelity attainable with state-of-the-art DNA-editing procedures. Finally, we identify areas that warrant further investigation.
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Affiliation(s)
- Ignazio Maggio
- Leiden University Medical Center, Department of Molecular Cell Biology, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Manuel A F V Gonçalves
- Leiden University Medical Center, Department of Molecular Cell Biology, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
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16
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Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G. Visualizing phosphodiester-bond hydrolysis by an endonuclease. Nat Struct Mol Biol 2014; 22:65-72. [PMID: 25486305 DOI: 10.1038/nsmb.2932] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/12/2014] [Indexed: 01/12/2023]
Abstract
The enzymatic hydrolysis of DNA phosphodiester bonds has been widely studied, but the chemical reaction has not yet been observed. Here we follow the generation of a DNA double-strand break (DSB) by the Desulfurococcus mobilis homing endonuclease I-DmoI, trapping sequential stages of a two-metal-ion cleavage mechanism. We captured intermediates of the different catalytic steps, and this allowed us to watch the reaction by 'freezing' multiple states. We observed the successive entry of two metals involved in the reaction and the arrival of a third cation in a central position of the active site. This third metal ion has a crucial role, triggering the consecutive hydrolysis of the targeted phosphodiester bonds in the DNA strands and leaving its position once the DSB is generated. The multiple structures show the orchestrated conformational changes in the protein residues, nucleotides and metals during catalysis.
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Affiliation(s)
- Rafael Molina
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Stefano Stella
- 1] Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. [2] Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pilar Redondo
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Hansel Gomez
- Joint Barcelona Computing Center (BSC)-Centre for Genomic Regulation (CRG)-Institute for Research in Biomedicine (IRB) Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
| | - María José Marcaida
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Modesto Orozco
- 1] Joint Barcelona Computing Center (BSC)-Centre for Genomic Regulation (CRG)-Institute for Research in Biomedicine (IRB) Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. [2] Departament de Bioquimica, Facultat de Biologia, University of Barcelona, Barcelona, Spain
| | - Jesús Prieto
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Guillermo Montoya
- 1] Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. [2] Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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17
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Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Proc Natl Acad Sci U S A 2014; 111:17003-10. [PMID: 25378705 DOI: 10.1073/pnas.1414399111] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Chromosome engineering is a major focus in the fields of systems biology, genetics, synthetic biology, and the functional analysis of genomes. Here, we describe the "telomerator," a new synthetic biology device for use in Saccharomyces cerevisiae. The telomerator is designed to inducibly convert circular DNA molecules into mitotically stable, linear chromosomes replete with functional telomeres in vivo. The telomerator cassette encodes convergent yeast telomere seed sequences flanking the I-SceI homing endonuclease recognition site in the center of an intron artificially transplanted into the URA3 selectable/counterselectable auxotrophic marker. We show that inducible expression of the homing endonuclease efficiently generates linear molecules, identified by using a simple plate-based screening method. To showcase its functionality and utility, we use the telomerator to circularly permute a synthetic yeast chromosome originally constructed as a circular molecule, synIXR, to generate 51 linear variants. Many of the derived linear chromosomes confer unexpected phenotypic properties. This finding indicates that the telomerator offers a new way to study the effects of gene placement on chromosomes (i.e., telomere proximity). However, that the majority of synIXR linear derivatives support viability highlights inherent tolerance of S. cerevisiae to changes in gene order and overall chromosome structure. The telomerator serves as an important tool to construct artificial linear chromosomes in yeast; the concept can be extended to other eukaryotes.
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18
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Teimourian S, Abdollahzadeh R. Technology developments in biological tools for targeted genome surgery. Biotechnol Lett 2014; 37:29-39. [PMID: 25257583 DOI: 10.1007/s10529-014-1656-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 08/29/2014] [Indexed: 12/26/2022]
Abstract
Different biological tools for targeted genome engineering have recently appeared and these include tools like meganucleases, zinc-finger nucleases and newer technologies including TALENs and CRISPR/Cas systems. transcription activator-like effector nucleases (TALENs) have greatly improved genome editing efficiency by making site-specific DNA double-strand breaks. Several studies have shown the prominence of TALENs in comparison to the meganucleases and zinc-finger nucleases. The most important feature of TALENs that makes them suitable tools for targeted genome editing is the modularity of central repeat domains, meaning that they can be designed to recognize any desirable DNA sequence. In this review, we present a comprehensive and concise description of TALENs technology developments for targeted genome surgery with to the point description and comparison of other tools.
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Affiliation(s)
- Shahram Teimourian
- Department of Medical Genetics, Iran University of Medical Sciences, Tehran, Iran,
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19
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Li MV, Shukla D, Rhodes BH, Lall A, Shu J, Moriarity BS, Largaespada DA. HomeRun Vector Assembly System: a flexible and standardized cloning system for assembly of multi-modular DNA constructs. PLoS One 2014; 9:e100948. [PMID: 24959875 PMCID: PMC4069157 DOI: 10.1371/journal.pone.0100948] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 06/01/2014] [Indexed: 11/29/2022] Open
Abstract
Advances in molecular and synthetic biology call for efficient assembly of multi-modular DNA constructs. We hereby present a novel modular cloning method that obviates the need for restriction endonucleases and significantly improves the efficiency in the design and construction of complex DNA molecules by standardizing all DNA elements and cloning reactions. Our system, named HomeRun Vector Assembly System (HVAS), employs a three-tiered vector series that utilizes both multisite gateway cloning and homing endonucleases, with the former building individual functional modules and the latter linking modules into the final construct. As a proof-of-principle, we first built a two-module construct that supported doxycycline-induced expression of green fluorescent protein (GFP). Further, with a three-module construct we showed quantitatively that there was minimal promoter leakage between neighbouring modules. Finally, we developed a method, in vitro Cre recombinase-mediated cassette exchange (RMCE) cloning, to regenerate a gateway destination vector from a previous multisite gateway cloning reaction, allowing access to existing DNA element libraries in conventional gateway entry clones, and simple creation of constructs ready for in vivo RMCE. We believe these methods constitute a useful addition to the standard molecular cloning techniques that could potentially support industrial scale synthesis of DNA constructs.
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Affiliation(s)
- Ming V. Li
- Division of Endocrinology and Diabetes, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail:
| | - Dip Shukla
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Brian H. Rhodes
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Anjali Lall
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jingmin Shu
- Division of Endocrinology and Diabetes, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Genome Engineering and Institute of Human Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Branden S. Moriarity
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Genome Engineering and Institute of Human Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - David A. Largaespada
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Genome Engineering and Institute of Human Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
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20
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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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21
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Simoni A, Siniscalchi C, Chan YS, Huen DS, Russell S, Windbichler N, Crisanti A. Development of synthetic selfish elements based on modular nucleases in Drosophila melanogaster. Nucleic Acids Res 2014; 42:7461-72. [PMID: 24803674 PMCID: PMC4066794 DOI: 10.1093/nar/gku387] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Selfish genes are DNA elements that increase their rate of genetic transmission at the expense of other genes in the genome and can therefore quickly spread within a population. It has been suggested that selfish elements could be exploited to modify the genome of entire populations for medical and ecological applications. Here we report that transcription activator-like effector nuclease (TALEN) and zinc finger nuclease (ZFN) can be engineered into site-specific synthetic selfish elements (SSEs) and demonstrate their transmission of up to 70% in the Drosophila germline. We show here that SSEs can spread via DNA break-induced homologous recombination, a process known as 'homing' similar to that observed for homing endonuclease genes (HEGs), despite their fundamentally different modes of DNA binding and cleavage. We observed that TALEN and ZFN have a reduced capability of secondary homing compared to HEG as their repetitive structure had a negative effect on their genetic stability. The modular architecture of ZFNs and TALENs allows for the rapid design of novel SSEs against specific genomic sequences making them potentially suitable for the genetic engineering of wild-type populations of animals and plants, in applications such as gene replacement or population suppression of pest species.
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Affiliation(s)
- Alekos Simoni
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Carla Siniscalchi
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Yuk-Sang Chan
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - David S Huen
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Steven Russell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre of FunctionalGenomics, University of Perugia, S. Andrea delle Fratte, 06132, Perugia, Italy
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22
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Guha TK, Hausner G. A homing endonuclease with a switch: Characterization of a twintron encoded homing endonuclease. Fungal Genet Biol 2014; 65:57-68. [DOI: 10.1016/j.fgb.2014.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 10/25/2022]
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23
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Redondo P, Merino N, Villate M, Blanco FJ, Montoya G, Molina R. Crystallization and preliminary X-ray diffraction analysis of the homing endonuclease I-CvuI from Chlorella vulgaris in complex with its target DNA. Acta Crystallogr F Struct Biol Commun 2014; 70:256-9. [PMID: 24637769 PMCID: PMC3936450 DOI: 10.1107/s2053230x1400065x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/10/2014] [Indexed: 11/10/2022] Open
Abstract
Homing endonucleases are highly specific DNA-cleaving enzymes that recognize long stretches of DNA. The engineering of these enzymes provides novel instruments for genome modification in a wide range of fields, including gene targeting, by inducing specific double-strand breaks. I-CvuI is a homing endonuclease from the green alga Chlorella vulgaris. This enzyme was purified after overexpression in Escherichia coli. Crystallization experiments of I-CvuI in complex with its DNA target in the presence of Mg(2+) yielded crystals suitable for X-ray diffraction analysis. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 62.83, b = 83.56, c = 94.40 Å. The self-rotation function and the Matthews coefficient suggested the presence of one protein-DNA complex per asymmetric unit. The crystals diffracted to a resolution limit of 1.9 Å using synchrotron radiation.
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Affiliation(s)
- Pilar Redondo
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez Almagro 3, 28029 Madrid, Spain
| | - Nekane Merino
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Vizcaya, Edificio 800, 48160 Derio, Spain
| | - Maider Villate
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Vizcaya, Edificio 800, 48160 Derio, Spain
| | - Francisco J. Blanco
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Vizcaya, Edificio 800, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Alameda Urquijo 36-5, 48011 Bilbao, Spain
| | - Guillermo Montoya
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez Almagro 3, 28029 Madrid, Spain
| | - Rafael Molina
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez Almagro 3, 28029 Madrid, Spain
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24
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Hafez M, Guha TK, Shen C, Sethuraman J, Hausner G. PCR-based bioprospecting for homing endonucleases in fungal mitochondrial rRNA genes. Methods Mol Biol 2014; 1123:37-53. [PMID: 24510258 DOI: 10.1007/978-1-62703-968-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Fungal mitochondrial genomes act as "reservoirs" for homing endonucleases. These enzymes with their DNA site-specific cleavage activities are attractive tools for genome editing and gene therapy applications. Bioprospecting and characterization of naturally occurring homing endonucleases offers an alternative to synthesizing artificial endonucleases. Here, we describe methods for PCR-based screening of fungal mitochondrial rRNA genes for homing endonuclease encoding sequences, and we also provide protocols for the purification and biochemical characterization of putative native homing endonucleases.
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Affiliation(s)
- Mohamed Hafez
- Department of Biochemistry, Université de Montréal, Montréal, QC, Canada
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25
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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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26
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Abstract
Homing endonucleases are strong drivers of genetic exchange and horizontal transfer of both their own genes and their local genetic environment. The mechanisms that govern the function and evolution of these genetic oddities have been well documented over the past few decades at the genetic, biochemical, and structural levels. This wealth of information has led to the manipulation and reprogramming of the endonucleases and to their exploitation in genome editing for use as therapeutic agents, for insect vector control and in agriculture. In this chapter we summarize the molecular properties of homing endonucleases and discuss their strengths and weaknesses in genome editing as compared to other site-specific nucleases such as zinc finger endonucleases, TALEN, and CRISPR-derived endonucleases.
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27
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Yanik M, Alzubi J, Lahaye T, Cathomen T, Pingoud A, Wende W. TALE-PvuII fusion proteins--novel tools for gene targeting. PLoS One 2013; 8:e82539. [PMID: 24349308 PMCID: PMC3857828 DOI: 10.1371/journal.pone.0082539] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/01/2013] [Indexed: 12/15/2022] Open
Abstract
Zinc finger nucleases (ZFNs) consist of zinc fingers as DNA-binding module and the non-specific DNA-cleavage domain of the restriction endonuclease FokI as DNA-cleavage module. This architecture is also used by TALE nucleases (TALENs), in which the DNA-binding modules of the ZFNs have been replaced by DNA-binding domains based on transcription activator like effector (TALE) proteins. Both TALENs and ZFNs are programmable nucleases which rely on the dimerization of FokI to induce double-strand DNA cleavage at the target site after recognition of the target DNA by the respective DNA-binding module. TALENs seem to have an advantage over ZFNs, as the assembly of TALE proteins is easier than that of ZFNs. Here, we present evidence that variant TALENs can be produced by replacing the catalytic domain of FokI with the restriction endonuclease PvuII. These fusion proteins recognize only the composite recognition site consisting of the target site of the TALE protein and the PvuII recognition sequence (addressed site), but not isolated TALE or PvuII recognition sites (unaddressed sites), even at high excess of protein over DNA and long incubation times. In vitro, their preference for an addressed over an unaddressed site is > 34,000-fold. Moreover, TALE-PvuII fusion proteins are active in cellula with minimal cytotoxicity.
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Affiliation(s)
- Mert Yanik
- Institute for Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany
| | - Jamal Alzubi
- Institute for Cell and Gene Therapy, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Thomas Lahaye
- ZMBP – General Genetics, University of Tuebingen, Tuebingen, Germany
| | - Toni Cathomen
- Institute for Cell and Gene Therapy, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Alfred Pingoud
- Institute for Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany
| | - Wolfgang Wende
- Institute for Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany
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28
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Evolutionary dynamics of introns and their open reading frames in the U7 region of the mitochondrial rnl gene in species of Ceratocystis. Fungal Biol 2013; 117:791-806. [DOI: 10.1016/j.funbio.2013.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 10/12/2013] [Accepted: 10/14/2013] [Indexed: 12/31/2022]
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29
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Deussing JM. Targeted mutagenesis tools for modelling psychiatric disorders. Cell Tissue Res 2013; 354:9-25. [PMID: 24078022 DOI: 10.1007/s00441-013-1708-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/16/2013] [Indexed: 12/15/2022]
Abstract
In the 1980s, the basic principles of gene targeting were discovered and forged into sharp tools for efficient and precise engineering of the mouse genome. Since then, genetic mouse models have substantially contributed to our understanding of major neurobiological concepts and are of utmost importance for our comprehension of neuropsychiatric disorders. The "domestication" of site-specific recombinases and the continuous creative technological developments involving the implementation of previously identified biological principles such as transcriptional and posttranslational control now enable conditional mutagenesis with high spatial and temporal resolution. The initiation and successful accomplishment of large-scale efforts to annotate functionally the entire mouse genome and to build strategic resources for the research community have significantly accelerated the rapid proliferation and broad propagation of mouse genetic tools. Addressing neurobiological processes with the assistance of genetic mouse models is a routine procedure in psychiatric research and will be further extended in order to improve our understanding of disease mechanisms. In light of the highly complex nature of psychiatric disorders and the current lack of strong causal genetic variants, a major future challenge is to model of psychiatric disorders more appropriately. Humanized mice, and the recently developed toolbox of site-specific nucleases for more efficient and simplified tailoring of the genome, offer the perspective of significantly improved models. Ultimately, these tools will push the limits of gene targeting beyond the mouse to allow genome engineering in any model organism of interest.
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Affiliation(s)
- Jan M Deussing
- Max Planck Institute of Psychiatry, Molecular Neurogenetics, Kraepelinstrasse 2-10, 80804, Munich, Germany,
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30
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Wirth T, Parker N, Ylä-Herttuala S. History of gene therapy. Gene 2013; 525:162-9. [PMID: 23618815 DOI: 10.1016/j.gene.2013.03.137] [Citation(s) in RCA: 321] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 12/24/2022]
Abstract
Two decades after the initial gene therapy trials and more than 1700 approved clinical trials worldwide we not only have gained much new information and knowledge regarding gene therapy in general, but also learned to understand the concern that has persisted in society. Despite the setbacks gene therapy has faced, success stories have increasingly emerged. Examples for these are the positive recommendation for a gene therapy product (Glybera) by the EMA for approval in the European Union and the positive trials for the treatment of ADA deficiency, SCID-X1 and adrenoleukodystrophy. Nevertheless, our knowledge continues to grow and during the course of time more safety data has become available that helps us to develop better gene therapy approaches. Also, with the increased understanding of molecular medicine, we have been able to develop more specific and efficient gene transfer vectors which are now producing clinical results. In this review, we will take a historical view and highlight some of the milestones that had an important impact on the development of gene therapy. We will also discuss briefly the safety and ethical aspects of gene therapy and address some concerns that have been connected with gene therapy as an important therapeutic modality.
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Affiliation(s)
- Thomas Wirth
- A.I. Virtanen Institute, Biotechnology and Molecular Medicine Unit, Univ. of Eastern Finland, Kuopio, Finland
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31
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Gabsalilow L, Schierling B, Friedhoff P, Pingoud A, Wende W. Site- and strand-specific nicking of DNA by fusion proteins derived from MutH and I-SceI or TALE repeats. Nucleic Acids Res 2013; 41:e83. [PMID: 23408850 PMCID: PMC3627573 DOI: 10.1093/nar/gkt080] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Targeted genome engineering requires nucleases that introduce a highly specific double-strand break in the genome that is either processed by homology-directed repair in the presence of a homologous repair template or by non-homologous end-joining (NHEJ) that usually results in insertions or deletions. The error-prone NHEJ can be efficiently suppressed by ‘nickases’ that produce a single-strand break rather than a double-strand break. Highly specific nickases have been produced by engineering of homing endonucleases and more recently by modifying zinc finger nucleases (ZFNs) composed of a zinc finger array and the catalytic domain of the restriction endonuclease FokI. These ZF-nickases work as heterodimers in which one subunit has a catalytically inactive FokI domain. We present two different approaches to engineer highly specific nickases; both rely on the sequence-specific nicking activity of the DNA mismatch repair endonuclease MutH which we fused to a DNA-binding module, either a catalytically inactive variant of the homing endonuclease I-SceI or the DNA-binding domain of the TALE protein AvrBs4. The fusion proteins nick strand specifically a bipartite recognition sequence consisting of the MutH and the I-SceI or TALE recognition sequences, respectively, with a more than 1000-fold preference over a stand-alone MutH site. TALE–MutH is a programmable nickase.
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Affiliation(s)
- Lilia Gabsalilow
- Institute for Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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32
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Schenkwein D, Turkki V, Ahlroth MK, Timonen O, Airenne KJ, Ylä-Herttuala S. rDNA-directed integration by an HIV-1 integrase--I-PpoI fusion protein. Nucleic Acids Res 2012; 41:e61. [PMID: 23275537 PMCID: PMC3597653 DOI: 10.1093/nar/gks1438] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Integrating viral vectors are efficient gene transfer tools, but their integration patterns have been associated with genotoxicity and oncogenicity. The recent development of highly specific designer nucleases has enabled target DNA modification and site-specific gene insertion at desired genomic loci. However, a lack of consensus exists regarding a perfect genomic safe harbour (GSH) that would allow transgenes to be stably and reliably expressed without adversely affecting endogenous gene structure and function. Ribosomal DNA (rDNA) has many advantages as a GSH, but efficient means to target integration to this locus are currently lacking. We tested whether lentivirus vector integration can be directed to rDNA by using fusion proteins consisting of the Human Immunodeficiency Virus 1 (HIV-1) integrase (IN) and the homing endonuclease I-PpoI, which has natural cleavage sites in the rDNA. A point mutation (N119A) was introduced into I-PpoI to abolish unwanted DNA cleavage by the endonuclease. The vector-incorporated IN-I-PpoIN119A fusion protein targeted integration into rDNA significantly more than unmodified lentivirus vectors, with an efficiency of 2.7%. Our findings show that IN-fusion proteins can be used to modify the integration pattern of lentivirus vectors, and to package site-specific DNA-recognizing proteins into vectors to obtain safer transgene integration.
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Affiliation(s)
- Diana Schenkwein
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland.
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Karimova M, Abi-Ghanem J, Berger N, Surendranath V, Pisabarro MT, Buchholz F. Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system. Nucleic Acids Res 2012; 41:e37. [PMID: 23143104 PMCID: PMC3553980 DOI: 10.1093/nar/gks1037] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Targeted genome engineering has become an important research area for diverse disciplines, with site-specific recombinases (SSRs) being among the most popular genome engineering tools. Their ability to trigger excision, integration, inversion and translocation has made SSRs an invaluable tool to manipulate DNA in vitro and in vivo. However, sophisticated strategies that combine different SSR systems are ever increasing. Hence, the demand for additional precise and efficient recombinases is dictated by the increasing complexity of the genetic studies. Here, we describe a novel site-specific recombination system designated Vika/vox. Vika originates from a degenerate bacteriophage of Vibrio coralliilyticus and shares low sequence similarity to other tyrosine recombinases, but functionally carries out a similar type of reaction. We demonstrate that Vika is highly specific in catalyzing vox recombination without recombining target sites from other SSR systems. We also compare the recombination activity of Vika/vox with other SSR systems, providing a guideline for deciding on the most suitable enzyme for a particular application and demonstrate that Vika expression does not cause cytotoxicity in mammalian cells. Our results show that Vika/vox is a novel powerful and safe instrument in the 'genetic toolbox' that can be used alone or in combination with other SSRs in heterologous hosts.
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Affiliation(s)
- Madina Karimova
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, University of Technology, Fetscherstrasse 74, 01307 Dresden, Germany
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Villate M, Merino N, Blanco FJ. Production of meganucleases by cell-free protein synthesis for functional and structural studies. Protein Expr Purif 2012; 85:246-9. [PMID: 22917812 DOI: 10.1016/j.pep.2012.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 07/16/2012] [Accepted: 07/24/2012] [Indexed: 11/30/2022]
Abstract
Meganucleases are highly specific endonucleases that recognize and cleave long DNA sequences, making them powerful tools for gene targeting. We describe the production of active recombinant meganucleases suitable for functional and structural studies using a batch-based cell-free protein synthesis method. Isotopic labeling of the I-CreI meganuclease is demonstrated opening the way for structural and ligand binding studies in solution by nuclear magnetic resonance (NMR)(2) which was previously hampered by the problems associated with the toxicity of the enzyme for Escherichia coli limiting its growth. The method can be adapted for the synthesis of soluble engineered variants that are produced as inclusion bodies in bacterial cells, thus facilitating their purification as soluble proteins instead of using denaturing-refolding protocols.
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Affiliation(s)
- Maider Villate
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Derio, Spain
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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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36
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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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Meiring TL, Tuffin IM, Cary C, Cowan DA. Genome sequence of temperate bacteriophage Psymv2 from Antarctic Dry Valley soil isolate Psychrobacter sp. MV2. Extremophiles 2012; 16:715-26. [PMID: 22760730 DOI: 10.1007/s00792-012-0467-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 06/14/2012] [Indexed: 11/24/2022]
Abstract
A temperate phage, Psymv2, was isolated from an Antarctic soil bacterium, Psychrobacter sp. MV2. The morphology of Psymv2 was typical of the Siphoviridae, with an isometric head and non-contractile tail. The Psymv2 genome was found to be 35,725 bp in length, had a G + C content of 44.5 %, with 49 protein-coding genes and one tRNA gene predicted. Integration of Psymv2 occurred at an ssrA gene, with the last 27 bases of this gene directly repeated at the prophage ends. The genome was organised in a modular fashion: integration, regulation, packaging, head assembly, tail assembly, host specificity and lysis. While the genome sequence had little similarity on a nucleotide level to previously reported phage sequences, the genome architecture resembled that of Siphoviridae of low G + C Gram-positive bacteria. The closest relatives to Psymv2 were uncharacterized putative prophages within the P. arcticus 273-4 and Acinetobacter baumannii 6013113 genomes. Global alignment of the Psymv2 genome and these prophages revealed significant conservation of the structural modules despite the large spatial divergence of their hosts. A number of unique ORFs were identified in the Psymv2 genome that may contribute to phage and lysogen fitness.
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Affiliation(s)
- Tracy L Meiring
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Office 2117, Level 2 Life Sciences Building, Modderdam Rd, Bellville 7535, South Africa
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Komiyama M, Sumaoka J. Design and Applications of Artificial Restriction DNA Cutters for Site-Selective Scission of Genomes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2012. [DOI: 10.1246/bcsj.20110318] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo
| | - Jun Sumaoka
- Research Center for Advanced Science and Technology, The University of Tokyo
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Abstract
Targeted manipulation of complex genomes often requires the introduction of a double-strand break at defined locations by site-specific DNA endonucleases. Here, we describe a monomeric nuclease domain derived from GIY-YIG homing endonucleases for genome-editing applications. Fusion of the GIY-YIG nuclease domain to three-member zinc-finger DNA binding domains generated chimeric GIY-zinc finger endonucleases (GIY-ZFEs). Significantly, the I-TevI-derived fusions (Tev-ZFEs) function in vitro as monomers to introduce a double-strand break, and discriminate in vitro and in bacterial and yeast assays against substrates lacking a preferred 5'-CNNNG-3' cleavage motif. The Tev-ZFEs function to induce recombination in a yeast-based assay with activity on par with a homodimeric Zif268 zinc-finger nuclease. We also fused the I-TevI nuclease domain to a catalytically inactive LADGLIDADG homing endonuclease (LHE) scaffold. The monomeric Tev-LHEs are active in vivo and similarly discriminate against substrates lacking the 5'-CNNNG-3' motif. The monomeric Tev-ZFEs and Tev-LHEs are distinct from the FokI-derived zinc-finger nuclease and TAL effector nuclease platforms as the GIY-YIG domain alleviates the requirement to design two nuclease fusions to target a given sequence, highlighting the diversity of nuclease domains with distinctive biochemical properties suitable for genome-editing applications.
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40
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Molina R, Redondo P, Stella S, Marenchino M, D’Abramo M, Gervasio FL, Charles Epinat J, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G. Non-specific protein-DNA interactions control I-CreI target binding and cleavage. Nucleic Acids Res 2012; 40:6936-45. [PMID: 22495931 PMCID: PMC3413129 DOI: 10.1093/nar/gks320] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Homing endonucleases represent protein scaffolds that provide powerful tools for genome manipulation, as these enzymes possess a very low frequency of DNA cleavage in eukaryotic genomes due to their high specificity. The basis of protein–DNA recognition must be understood to generate tailored enzymes that target the DNA at sites of interest. Protein–DNA interaction engineering of homing endonucleases has demonstrated the potential of these approaches to create new specific instruments to target genes for inactivation or repair. Protein–DNA interface studies have been focused mostly on specific contacts between amino acid side chains and bases to redesign the binding interface. However, it has been shown that 4 bp in the central DNA sequence of the 22-bp substrate of a homing endonuclease (I-CreI), which do not show specific protein–DNA interactions, is not devoid of content information. Here, we analyze the mechanism of target discrimination in this substrate region by the I-CreI protein, determining how it can occur independently of the specific protein–DNA interactions. Our data suggest the important role of indirect readout in this substrate region, opening the possibility for a fully rational search of new target sequences, thus improving the development of redesigned enzymes for therapeutic and biotechnological applications.
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Affiliation(s)
- Rafael Molina
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), NMR Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Computational Biophysics Group, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain and CELLECTIS S.A., 8 rue de la croix Jarry, 75013 Paris, France
| | - Pilar Redondo
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), NMR Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Computational Biophysics Group, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain and CELLECTIS S.A., 8 rue de la croix Jarry, 75013 Paris, France
| | - Stefano Stella
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), NMR Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Computational Biophysics Group, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain and CELLECTIS S.A., 8 rue de la croix Jarry, 75013 Paris, France
| | - Marco Marenchino
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), NMR Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Computational Biophysics Group, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain and CELLECTIS S.A., 8 rue de la croix Jarry, 75013 Paris, France
| | - Marco D’Abramo
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), NMR Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Computational Biophysics Group, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain and CELLECTIS S.A., 8 rue de la croix Jarry, 75013 Paris, France
| | - Francesco Luigi Gervasio
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), NMR Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Computational Biophysics Group, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain and CELLECTIS S.A., 8 rue de la croix Jarry, 75013 Paris, France
| | - Jean Charles Epinat
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), NMR Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Computational Biophysics Group, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain and CELLECTIS S.A., 8 rue de la croix Jarry, 75013 Paris, France
| | - Julien Valton
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), NMR Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Computational Biophysics Group, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain and CELLECTIS S.A., 8 rue de la croix Jarry, 75013 Paris, France
| | - Silvestre Grizot
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), NMR Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Computational Biophysics Group, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain and CELLECTIS S.A., 8 rue de la croix Jarry, 75013 Paris, France
| | - Phillipe Duchateau
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), NMR Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Computational Biophysics Group, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain and CELLECTIS S.A., 8 rue de la croix Jarry, 75013 Paris, France
| | - Jesús Prieto
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), NMR Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Computational Biophysics Group, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain and CELLECTIS S.A., 8 rue de la croix Jarry, 75013 Paris, France
- *To whom correspondence should be addressed. Tel: +34 91 2246900; Fax: +34 91 2246976;
| | - Guillermo Montoya
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), NMR Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Computational Biophysics Group, c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain and CELLECTIS S.A., 8 rue de la croix Jarry, 75013 Paris, France
- *To whom correspondence should be addressed. Tel: +34 91 2246900; Fax: +34 91 2246976;
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Gupta R, Capalash N, Sharma P. Restriction endonucleases: natural and directed evolution. Appl Microbiol Biotechnol 2012; 94:583-99. [PMID: 22398859 DOI: 10.1007/s00253-012-3961-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 02/08/2012] [Accepted: 02/09/2012] [Indexed: 10/28/2022]
Abstract
Type II restriction endonucleases (REs) are highly sequence-specific compared with other classes of nucleases. PD-(D/E)XK nucleases, initially represented by only type II REs, now comprise a large and extremely diverse superfamily of proteins and, although sharing a structurally conserved core, typically display little or no detectable sequence similarity except for the active site motifs. Sequence similarity can only be observed in methylases and few isoschizomers. As a consequence, REs are classified according to combinations of functional properties rather than on the basis of genetic relatedness. New alignment matrices and classification systems based on structural core connectivity and cleavage mechanisms have been developed to characterize new REs and related proteins. REs recognizing more than 300 distinct specificities have been identified in RE database (REBASE: http://rebase.neb.com/cgi-bin/statlist ) but still the need for newer specificities is increasing due to the advancement in molecular biology and applications. The enzymes have undergone constant evolution through structural changes in protein scaffolds which include random mutations, homologous recombinations, insertions, and deletions of coding DNA sequences but rational mutagenesis or directed evolution delivers protein variants with new functions in accordance with defined biochemical or environmental pressures. Redesigning through random mutation, addition or deletion of amino acids, methylation-based selection, synthetic molecules, combining recognition and cleavage domains from different enzymes, or combination with domains of additional functions change the cleavage specificity or substrate preference and stability. There is a growing number of patents awarded for the creation of engineered REs with new and enhanced properties.
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Affiliation(s)
- Richa Gupta
- Department of Biotechnology, Panjab University, Chandigarh, India 160014
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42
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Asuri P, Bartel MA, Vazin T, Jang JH, Wong TB, Schaffer DV. Directed evolution of adeno-associated virus for enhanced gene delivery and gene targeting in human pluripotent stem cells. Mol Ther 2012; 20:329-38. [PMID: 22108859 PMCID: PMC3277219 DOI: 10.1038/mt.2011.255] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 10/27/2011] [Indexed: 12/12/2022] Open
Abstract
Efficient approaches for the precise genetic engineering of human pluripotent stem cells (hPSCs) can enhance both basic and applied stem cell research. Adeno- associated virus (AAV) vectors are of particular interest for their capacity to mediate efficient gene delivery to and gene targeting in various cells. However, natural AAV serotypes offer only modest transduction of human embryonic and induced pluripotent stem cells (hESCs and hiPSCs), which limits their utility for efficiently manipulating the hPSC genome. Directed evolution is a powerful means to generate viral vectors with novel capabilities, and we have applied this approach to create a novel AAV variant with high gene delivery efficiencies (~50%) to hPSCs, which are importantly accompanied by a considerable increase in gene-targeting frequencies, up to 0.12%. While this level is likely sufficient for numerous applications, we also show that the gene-targeting efficiency mediated by an evolved AAV variant can be further enhanced (>1%) in the presence of targeted double- stranded breaks (DSBs) generated by the co-delivery of artificial zinc finger nucleases (ZFNs). Thus, this study demonstrates that under appropriate selective pressures, AAV vectors can be created to mediate efficient gene targeting in hPSCs, alone or in the presence of ZFN- mediated double-stranded DNA breaks.
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Affiliation(s)
- Prashanth Asuri
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720-1462, USA
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43
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Affiliation(s)
- Jesús Prieto
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fdez Almagro, Madrid, Spain
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44
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The highly variable mitochondrial small-subunit ribosomal RNA gene of Ophiostoma minus. Fungal Biol 2011; 115:1122-37. [DOI: 10.1016/j.funbio.2011.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 05/28/2011] [Accepted: 07/15/2011] [Indexed: 12/18/2022]
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45
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McManus HA, Lewis LA, Fučíková K, Haugen P. Invasion of protein coding genes by green algal ribosomal group I introns. Mol Phylogenet Evol 2011; 62:109-16. [PMID: 22056605 DOI: 10.1016/j.ympev.2011.09.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 06/04/2011] [Accepted: 09/17/2011] [Indexed: 11/25/2022]
Abstract
The spread of group I introns depends on their association with intron-encoded homing endonucleases. Introns that encode functional homing endonuclease genes (HEGs) are highly invasive, whereas introns that only encode the group I ribozyme responsible for self-splicing are generally stably inherited (i.e., vertical inheritance). A number of recent case studies have provided new knowledge on the evolution of group I introns, however, there are still large gaps in understanding of their distribution on the tree of life, and how they have spread into new hosts and genic sites. During a larger phylogenetic survey of chlorophyceaen green algae, we found that 23 isolates contain at least one group I intron in the rbcL chloroplast gene. Structural analyses show that the introns belong to one of two intron lineages, group IA2 intron-HEG (GIY-YIG family) elements inserted after position 462 in the rbcL gene, and group IA1 introns inserted after position 699. The latter intron type sometimes encodes HNH homing endonucleases. The distribution of introns was analyzed on an exon phylogeny and patterns were recovered that are consistent with vertical inheritance and possible horizontal transfer. The rbcL 462 introns are thus far reported only within the Volvocales, Hydrodictyaceae and Bracteacoccus, and closely related isolates of algae differ in the presence of rbcL introns. Phylogenetic analysis of the intron conserved regions indicates that the rbcL699 and rbcL462 introns have distinct evolutionary origins. The rbcL699 introns were likely derived from ribosomal RNA L2449 introns, whereas the rbcL462 introns form a close relationship with psbA introns.
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Affiliation(s)
- Hilary A McManus
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Rd., Storrs, CT 06269, USA.
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46
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Fonfara I, Curth U, Pingoud A, Wende W. Creating highly specific nucleases by fusion of active restriction endonucleases and catalytically inactive homing endonucleases. Nucleic Acids Res 2011; 40:847-60. [PMID: 21965534 PMCID: PMC3258161 DOI: 10.1093/nar/gkr788] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Zinc-finger nucleases and TALE nucleases are produced by combining a specific DNA-binding module and a non-specific DNA-cleavage module, resulting in nucleases able to cleave DNA at a unique sequence. Here a new approach for creating highly specific nucleases was pursued by fusing a catalytically inactive variant of the homing endonuclease I-SceI, as DNA binding-module, to the type IIP restriction enzyme PvuII, as cleavage module. The fusion enzymes were designed to recognize a composite site comprising the recognition site of PvuII flanked by the recognition site of I-SceI. In order to reduce activity on PvuII sites lacking the flanking I-SceI sites, the enzymes were optimized so that the binding of I-SceI to its sites positions PvuII for cleavage of the composite site. This was achieved by optimization of the linker and by introducing amino acid substitutions in PvuII which decrease its activity or disturb its dimer interface. The most specific variant showed a more than 1000-fold preference for the addressed composite site over an unaddressed PvuII site. These results indicate that using a specific restriction enzyme, such as PvuII, as cleavage module, offers an alternative to the otherwise often used catalytic domain of FokI, which by itself does not contribute to the specificity of the engineered nuclease.
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Affiliation(s)
- Ines Fonfara
- Institut für Biochemie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 58, D-35392, Giessen, Germany
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47
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Winckler T. [Fight against malaria with genetically modified mosquitoes]. PHARMAZIE IN UNSERER ZEIT 2011; 40:374-375. [PMID: 22299152 DOI: 10.1002/pauz.201190056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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Tapping natural reservoirs of homing endonucleases for targeted gene modification. Proc Natl Acad Sci U S A 2011; 108:13077-82. [PMID: 21784983 DOI: 10.1073/pnas.1107719108] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Homing endonucleases mobilize their own genes by generating double-strand breaks at individual target sites within potential host DNA. Because of their high specificity, these proteins are used for "genome editing" in higher eukaryotes. However, alteration of homing endonuclease specificity is quite challenging. Here we describe the identification and phylogenetic analysis of over 200 naturally occurring LAGLIDADG homing endonucleases (LHEs). Biochemical and structural characterization of endonucleases from one clade within the phylogenetic tree demonstrates strong conservation of protein structure contrasted against highly diverged DNA target sites and indicates that a significant fraction of these proteins are sufficiently stable and active to serve as engineering scaffolds. This information was exploited to create a targeting enzyme to disrupt the endogenous monoamine oxidase B gene in human cells. The ubiquitous presence and diversity of LHEs described in this study may facilitate the creation of many tailored nucleases for genome editing.
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Mansilla-Soto J, Rivière I, Sadelain M. Genetic strategies for the treatment of sickle cell anaemia. Br J Haematol 2011; 154:715-27. [DOI: 10.1111/j.1365-2141.2011.08773.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Aiba Y, Sumaoka J, Komiyama M. Artificial DNA cutters for DNA manipulation and genome engineering. Chem Soc Rev 2011; 40:5657-68. [PMID: 21566825 DOI: 10.1039/c1cs15039a] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This tutorial review provides recent developments in artificial cutters for site-selective scission of DNA with the focus on chemistry-based DNA cutters. They are useful tools for molecular biology and biotechnology, since their site-selectivity of scission is much higher than that of naturally occurring restriction enzymes and also their scission site is freely chosen. In order to prepare these cutters, a DNA-cutting molecule is combined with a sequence-recognizing molecule in a covalent or non-covalent way. At targeted sites in single-stranded and double-stranded DNAs, the scission occurs via either oxidative cleavage of nucleotides or hydrolysis of phosphodiester linkages. Among many successful examples, an artificial restriction DNA cutter, prepared from Ce(iv)/EDTA and pseudo-complementary peptide nucleic acid, hydrolyzed double-stranded DNA at the target site. The scission site and scission specificity are determined simply in terms of the Watson-Crick rule so that even the whole genome of human beings was selectively cut at one predetermined site. Consistently, homologous recombination in human cells was successfully promoted by this tool. For the purpose of comparison, protein-based DNA cutters (e.g., zinc finger nucleases) are also briefly described. The potential applications of these cutters and their future aspects are discussed.
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Affiliation(s)
- Yuichiro Aiba
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
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