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Cho H, Oh DE, Côté S, Lee CS, Kim TH. Orientation-Guided Immobilization of Probe DNA on swCNT-FET for Enhancing Sensitivity of EcoRV Detection. Nano Lett 2024; 24:1901-1908. [PMID: 38147528 DOI: 10.1021/acs.nanolett.3c03877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
We present a novel approach that integrates electrical measurements with molecular dynamics (MD) simulations to assess the activity of type-II restriction endonucleases, specifically EcoRV. Our approach employs a single-walled carbon nanotube field-effect transistor (swCNT-FET) functionalized with the EcoRV substrate DNA, enabling the detection of enzymatic cleavage events. Notably, we leveraged the methylene blue (MB) tag as an "orientation guide" to immobilize the EcoRV substrate DNA in a specific direction, thereby enhancing the proximity of the DNA cleavage reaction to the swCNT surface and consequently improving the sensitivity in EcoRV detection. We conducted computational modeling to compare the conformations and electrostatic potential (ESP) of MB-tagged DNA with its MB-free counterpart, providing strong support for our electrical measurements. Both conformational and ESP simulations exhibited robust agreement with our experimental data. The inhibitory efficacy of the EcoRV inhibitor aurintricarboxylic acid (ATA) was also evaluated, and the selectivity of the sensing device was examined.
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Affiliation(s)
- Hyunju Cho
- Department of Chemistry, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Da Eun Oh
- Department of Chemistry, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Sébastien Côté
- Département de Physique, Faculté des Arts et des Sciences, Université de Montréal, Montréal H2 V 0B3, Canada
- Département de Physique, Cégep de Saint-Jérôme, Saint-Jérôme J7Z 4 V2, Canada
| | - Chang-Seuk Lee
- Department of Chemistry, Seoul Women's University, Seoul 01797, Republic of Korea
| | - Tae Hyun Kim
- Department of Chemistry, Soonchunhyang University, Asan 31538, Republic of Korea
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2
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Liu Y, Xu C, Zhou H, Wang W, Liu B, Li Y, Hu X, Yu F, He J. The crystal structures of Sau3AI with and without bound DNA suggest a self-activation-based DNA cleavage mechanism. Structure 2023; 31:1463-1472.e2. [PMID: 37652002 DOI: 10.1016/j.str.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 06/12/2023] [Accepted: 08/04/2023] [Indexed: 09/02/2023]
Abstract
The type II restriction endonuclease Sau3AI cleaves the sequence 5'-GATC-3' in double-strand DNA producing two sticky ends. Sau3AI cuts both DNA strands regardless of methylation status. Here, we report the crystal structures of the active site mutant Sau3AI-E64A and the C-terminal domain Sau3AI-C with a bound GATC substrate. Interestingly, the catalytic site of the N-terminal domain (Sau3AI-N) is spatially blocked by the C-terminal domain, suggesting a potential self-inhibition of the enzyme. Interruption of Sau3AI-C binding to substrate DNA disrupts Sau3AI function, suggesting a functional linkage between the N- and C-terminal domains. We propose that Sau3AI-C behaves as an allosteric effector binding one GATC substrate, which triggers a conformational change to open the N-terminal catalytic site, resulting in the subsequent GATC recognition by Sau3AI-N and cleavage of the second GATC site. Our data indicate that Sau3AI and UbaLAI might represent a new subclass of type IIE restriction enzymes.
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Affiliation(s)
- Yahui Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, China
| | - Chunyan Xu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Weiwei Wang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Bing Liu
- Department of Laboratory Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, China; Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Xiaojian Hu
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Feng Yu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
| | - Jianhua He
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.
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3
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Tasnim M, Selph TJ, Olcott J, Hill JT. The type IIS restriction enzyme MmeI can cut across a double-strand break. Mol Biol Rep 2023; 50:5495-5499. [PMID: 37031321 PMCID: PMC10209223 DOI: 10.1007/s11033-023-08375-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 03/07/2023] [Indexed: 04/10/2023]
Abstract
BACKGROUND Type-IIS restriction enzymes cut outside their recognition sites, allowing them to remove their binding sites upon digestion. This feature has resulted in their wide application in molecular biology techniques, including seamless cloning methods, enzymatic CRISPR library generation, and others. We studied the ability of the Type-IIS restriction enzyme MmeI, which recognizes an asymmetric sequence TCCRAC and cuts 20 bp downstream, to cut across a double-strand break (DSB). METHODS AND RESULTS We used synthetic double-stranded oligos with MmeI recognition sites close to 5' end and different overhang lengths to measure digestion after different periods of time and at different temperatures. We found that the MmeI binding and cutting sites can be situated on opposite sides of a DSB if the edges of the DNA molecules are held together by transient base-pairing interactions between compatible overhangs. CONCLUSION We found that MmeI can cut across a DSB, and the efficiency of the cutting depends on both overhang length and temperature.
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Affiliation(s)
- Maliha Tasnim
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, 4005, 84602, USA
| | - T Jacob Selph
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, 4005, 84602, USA
| | - Jason Olcott
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, 4005, 84602, USA
| | - Jonathon T Hill
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, 4005, 84602, USA.
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4
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Kennedy MA, Hosford CJ, Azumaya CM, Luyten YA, Chen M, Morgan RD, Stoddard BL. Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI. Nucleic Acids Res 2023; 51:4467-4487. [PMID: 36987874 PMCID: PMC10201449 DOI: 10.1093/nar/gkad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Type IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in biotechnology for a variety of purposes, including the creation of gene-targeting zinc finger and TAL effector nucleases and DNA synthesis applications such as Golden Gate assembly. The most thoroughly studied Type IIS enzyme, FokI, has been shown to require multimerization and engagement with multiple DNA targets for optimal cleavage activity; however, details of how it or similar enzymes forms a DNA-bound reaction complex have not been described at atomic resolution. Here we describe biochemical analyses of DNA cleavage by the Type IIS PaqCI restriction endonuclease and a series of molecular structures in the presence and absence of multiple bound DNA targets. The enzyme displays a similar tetrameric organization of target recognition domains in the absence or presence of bound substrate, with a significant repositioning of endonuclease domains in a trapped DNA-bound complex that is poised to deliver the first of a series of double-strand breaks. PaqCI and FokI share similar structural mechanisms of DNA cleavage, but considerable differences in their domain organization and quaternary architecture, facilitating comparisons between distinct Type IIS enzymes.
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Affiliation(s)
- Madison A Kennedy
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle,WA 98109, USA
| | | | - Caleigh M Azumaya
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle,WA 98109, USA
| | - Yvette A Luyten
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Minyong Chen
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | | | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle,WA 98109, USA
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5
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Malinin NL, Lee G, Lazzarotto CR, Li Y, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Iafrate AJ, Le LP, Aryee MJ, Joung JK, Tsai SQ. Defining genome-wide CRISPR-Cas genome-editing nuclease activity with GUIDE-seq. Nat Protoc 2021; 16:5592-5615. [PMID: 34773119 PMCID: PMC9331158 DOI: 10.1038/s41596-021-00626-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 09/02/2021] [Indexed: 12/26/2022]
Abstract
Genome-wide unbiased identification of double-stranded breaks enabled by sequencing (GUIDE-seq) is a sensitive, unbiased, genome-wide method for defining the activity of genome-editing nucleases in living cells. GUIDE-seq is based on the principle of efficient integration of an end-protected double-stranded oligodeoxynucleotide tag into sites of nuclease-induced DNA double-stranded breaks, followed by amplification of tag-containing genomic DNA molecules and high-throughput sequencing. Here we describe a detailed GUIDE-seq protocol including cell transfection, library preparation, sequencing and bioinformatic analysis. The entire protocol including cell culture can be completed in 9 d. Once tag-integrated genomic DNA is isolated, library preparation, sequencing and analysis can be performed in 3 d. The result is a genome-wide catalog of off-target sites ranked by nuclease activity as measured by GUIDE-seq read counts. GUIDE-seq is one of the most sensitive cell-based methods for defining genome-wide off-target activity and has been broadly adopted for research and therapeutic use.
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Affiliation(s)
- Nikolay L Malinin
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - GaHyun Lee
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cicera R Lazzarotto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yichao Li
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zongli Zheng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Nhu T Nguyen
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA
| | - Matthew Liebers
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Ved V Topkar
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - A John Iafrate
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Long P Le
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Martin J Aryee
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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6
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Deng J, Walther A. ATP-powered molecular recognition to engineer transient multivalency and self-sorting 4D hierarchical systems. Nat Commun 2020; 11:3658. [PMID: 32694613 PMCID: PMC7374688 DOI: 10.1038/s41467-020-17479-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023] Open
Abstract
Biological systems organize multiple hierarchical structures in parallel, and create dynamic assemblies and functions by energy dissipation. In contrast, emerging artificial non-equilibrium self-assembling systems have remained relatively simplistic concerning hierarchical design, and non-equilibrium multi-component systems are uncharted territory. Here we report a modular DNA toolbox allowing to program transient non-equilibrium multicomponent systems across hierarchical length scales by introducing chemically fueled molecular recognition orchestrated by reaction networks of concurrent ATP-powered ligation and cleavage of freely programmable DNA building blocks. Going across hierarchical levels, we demonstrate transient side-chain functionalized nucleic acid polymers, and further introduce the concept of transient cooperative multivalency as a key to bridge length scales to pioneer fuel-driven encapsulation, self-assembly of colloids, and non-equilibrium transient narcissistic colloidal self-sorting on a systems level. The fully programmable and functionalizable DNA components pave the way to design chemically fueled 4D (3 space, 1 time) molecular multicomponent systems and autonomous materials.
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Affiliation(s)
- Jie Deng
- A3BMS Lab, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104, Freiburg, Germany
- DFG Cluster of Excellence "Living, Adaptive and Energy-Autonomous Materials Systems" (livMatS), 79110, Freiburg, Germany
- Freiburg Materials Research Center, University of Freiburg, Stefan-Meier-Straße 21, 79104, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Albertstraße 19, 79104, Freiburg, Germany
| | - Andreas Walther
- A3BMS Lab, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104, Freiburg, Germany.
- DFG Cluster of Excellence "Living, Adaptive and Energy-Autonomous Materials Systems" (livMatS), 79110, Freiburg, Germany.
- Freiburg Materials Research Center, University of Freiburg, Stefan-Meier-Straße 21, 79104, Freiburg, Germany.
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany.
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Albertstraße 19, 79104, Freiburg, Germany.
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7
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Lin Y, Yang Z, Lake RJ, Zheng C, Lu Y. Enzyme-Mediated Endogenous and Bioorthogonal Control of a DNAzyme Fluorescent Sensor for Imaging Metal Ions in Living Cells. Angew Chem Int Ed Engl 2019; 58:17061-17067. [PMID: 31529664 PMCID: PMC7174831 DOI: 10.1002/anie.201910343] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Ren D, Fan M, Sun C, Zhou C, Li Y. Capillary Electrophoresis with Laser Induced Fluorescence Detection for Study of the Association of HSP60 Gene Polymorphism with Gouty Arthritis. J AOAC Int 2019; 102:810-814. [PMID: 30340651 DOI: 10.5740/jaoacint.18-0242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background: Gout arthritis is a common inflammatory arthritis and it poses a major threat to human health. Objective: A method of capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) for the detection of HSP60 gene polymorphism has been developed and applied to the exploration of correlation between gouty arthritis and HSP60 gene polymorphism. Methods: The genomic deoxyribonucleic acid from 59 patients with gouty arthritis and 64 control subjects was extracted and the conservative fragment of HSP60 was amplified. The products were digested with restriction endonuclease NlaIII and then separated and detected by the proposed method. Results: In the case group, there were 7 cases of TT genotype, 29 cases of CC genotype, and 23 cases of CT genotype. In the control group, there were 4 cases of TT genotype, 6 cases of CC genotype, and 54 cases of CT genotype. The detection results of the samples were statistically analyzed by binary logistic regression and Spearman correlation analysis. After adjusting gender, age, and other compounding factors, the TT genotype and CT genotype of the HSP60 gene were found to affect gouty arthritis. Conclusions: When used for gene polymorphism research, the proposed CE-LIF method has the advantages of high efficiency, rapidity, sensitivity, and low sample consumption. A moderate correlation between gouty arthritis and HSP60 genotype distribution was discovered for the first time. Highlights: A new method using CE-LIF for the detection of HSP60 gene polymorphism of 59 patients with gouty arthritis and 64 control subjects in China. The correlation between gouty arthritis and HSP60 gene polymorphism was explored for the first time.
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Affiliation(s)
- Dongxia Ren
- Sichuan University, West China School of Public Health, Chengdu, China 610044
| | - Min Fan
- Sichuan University, West China School of Public Health, Chengdu, China 610044
| | - Chengjun Sun
- Sichuan University, West China School of Public Health, Chengdu, China 610044
| | - Chen Zhou
- Sichuan University, West China School of Public Health, Chengdu, China 610044
| | - Yongxin Li
- Sichuan University, West China School of Public Health, Chengdu, China 610044
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9
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Tutkus M, Rakickas T, Kopu Stas A, Ivanovaitė ŠN, Venckus O, Navikas V, Zaremba M, Manakova E, Valiokas RN. Fixed DNA Molecule Arrays for High-Throughput Single DNA-Protein Interaction Studies. Langmuir 2019; 35:5921-5930. [PMID: 30955328 DOI: 10.1021/acs.langmuir.8b03424] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The DNA Curtains assay is a recently developed experimental platform for protein-DNA interaction studies at the single-molecule level that is based on anchoring and alignment of DNA fragments. The DNA Curtains so far have been made by using chromium barriers and fluid lipid bilayer membranes, which makes such a specialized assay technically challenging and relatively unstable. Herein, we report on an alternative strategy for DNA arraying for analysis of individual DNA-protein interactions. It relies on stable DNA tethering onto nanopatterned protein templates via high affinity molecular recognition. We describe fabrication of streptavidin templates (line features as narrow as 200 nm) onto modified glass coverslips by combining surface chemistry, atomic force microscopy (AFM), and soft lithography techniques with affinity-driven assembly. We have employed such chips for arraying single- and double-tethered DNA strands, and we characterized the obtained molecular architecture: we evaluated the structural characteristics and specific versus nonspecific binding of fluorescence-labeled DNA using AFM and total internal reflection fluorescence microscopy. We demonstrate the feasibility of our DNA molecule arrays for short single-tethered as well as for lambda single- and double-tethered DNA. The latter type of arrays proved very suitable for localization of single DNA-protein interactions employing restriction endonucleases. The presented molecular architecture and facile method of fabrication of our nanoscale platform does not require clean room equipment, and it offers advanced functional studies of DNA machineries and the development of future nanodevices.
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Affiliation(s)
| | | | - Aurimas Kopu Stas
- Vilnius University, Life Sciences Center, Institute of Biotechnology , Sauletekio av. 7 , Vilnius LT-10257 , Lithuania
| | | | | | | | - Mindaugas Zaremba
- Vilnius University, Life Sciences Center, Institute of Biotechnology , Sauletekio av. 7 , Vilnius LT-10257 , Lithuania
| | - Elena Manakova
- Vilnius University, Life Sciences Center, Institute of Biotechnology , Sauletekio av. 7 , Vilnius LT-10257 , Lithuania
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10
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Fu G, Fu L, Cai Y, Zhao H, Fu W. Association between polymorphisms of glucocorticoid receptor genes and asthma: A meta-analysis. Cell Mol Biol (Noisy-le-grand) 2018; 64:13-23. [PMID: 29729712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/19/2018] [Accepted: 03/24/2018] [Indexed: 06/08/2023]
Abstract
Recent studies have evaluated the associations between polymorphisms of glucocorticoid receptor genes and asthma. However, the conclusions of these studies are conflicting. The objective of this meta-analysis was to clarify the association between all known polymorphisms of glucocorticoid receptor genetic loci and susceptibility to asthma, based on existing reports. We conducted a meta-analysis of the association between glucocorticoid receptor polymorphisms (NR3C1) and asthma risk. A systematical literature search was performed in PubMed, EMBASE, Web of Science, China National Knowledge Infrastructure (CNKI), and Cochrane Library until January 15, 2018. The odds ratio (OR), 95% confidence interval (CI), and P value were calculated using Mantel-Haenszel statistics under the allele, homozygote, heterozygote, dominant, or recessive models. P values of less than 0.05 were considered to represent statistically significant associations between glucocorticoid receptor gene polymorphisms and asthma. All statistical analyses were done using the "meta" package (version 4.9-0) of R version 3.4.3 and RStudio version 1.0.44. A total of fourteen studies, reported via ten articles from online databases were included in our meta-analysis. For BclI (from eight studies), a significant association was detected in the allele model, homozygote model, and recessive model (C versus G: OR (95% CI) = 0.63 (0.40-0.97), CC versus GG: OR (95% CI) = 0.41(0.17-0.97), CC versus GC + GG: OR (95% CI) = 0.54(0.34-0.88)), but not in the heterozygote model or the dominant model. For ER22/23EK (from four studies), TthIII1 (from two studies), no significant association was found for any genetic model. After subgroup analyses by age, significant associations were observed for the allele model, homozygote model, dominant model and recessive model for BclI in adults. The ER22/23EK and TthIII1 polymorphisms were not found to be associated with susceptibility to ASTHMA; however, the BclI polymorphisms were significantly associated with ASTHMA in adults.
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Affiliation(s)
- Guanglei Fu
- Emergency Department, the first Affiliated Hospital of Jinan University, Guangzhou 510006, China
| | - Lijun Fu
- Department of anesthesiology, Shenzhen Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Youli Cai
- South China Research Center for Acupuncture and Moxibustion, School of basic medical science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hui Zhao
- South China Research Center for Acupuncture and Moxibustion, School of basic medical science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Wenjun Fu
- South China Research Center for Acupuncture and Moxibustion, School of basic medical science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
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11
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Yang F, Lei Y, Zhou M, Yao Q, Han Y, Wu X, Zhong W, Zhu C, Xu W, Tao R, Chen X, Lin D, Rahman K, Tyagi R, Habib Z, Xiao S, Wang D, Yu Y, Chen H, Fu Z, Cao G. Development and application of a recombination-based library versus library high- throughput yeast two-hybrid (RLL-Y2H) screening system. Nucleic Acids Res 2018; 46:e17. [PMID: 29165646 PMCID: PMC5815087 DOI: 10.1093/nar/gkx1173] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/13/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022] Open
Abstract
Protein-protein interaction (PPI) network maintains proper function of all organisms. Simple high-throughput technologies are desperately needed to delineate the landscape of PPI networks. While recent state-of-the-art yeast two-hybrid (Y2H) systems improved screening efficiency, either individual colony isolation, library preparation arrays, gene barcoding or massive sequencing are still required. Here, we developed a recombination-based 'library vs library' Y2H system (RLL-Y2H), by which multi-library screening can be accomplished in a single pool without any individual treatment. This system is based on the phiC31 integrase-mediated integration between bait and prey plasmids. The integrated fragments were digested by MmeI and subjected to deep sequencing to decode the interaction matrix. We applied this system to decipher the trans-kingdom interactome between Mycobacterium tuberculosis and host cells and further identified Rv2427c interfering with the phagosome-lysosome fusion. This concept can also be applied to other systems to screen protein-RNA and protein-DNA interactions and delineate signaling landscape in cells.
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Affiliation(s)
- Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingying Lei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Meiling Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qili Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yichao Han
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Wanshun Zhong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenghang Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Weize Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Ran Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Khaista Rahman
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Rohit Tyagi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zeshan Habib
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Dang Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Yu
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS, Beijing 100101, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenfang Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Departments of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
- Bio-Medical Center, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
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12
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Wu K, Ma C, Deng Z, Fang N, Tang Z, Zhu X, Wang K. Label-free and nicking enzyme-assisted fluorescence signal amplification for RNase H determination based on a G-quadruplexe/thioflavin T complex. Talanta 2018; 182:142-147. [PMID: 29501133 DOI: 10.1016/j.talanta.2018.01.075] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/13/2018] [Accepted: 01/29/2018] [Indexed: 12/21/2022]
Abstract
In this paper, we describe a novel, label-free and nicking enzyme-assisted fluorescence signal amplification strategy that demonstrates to be cost efficient, sensitive, and unique for assaying the RNase H activity and inhibition based on G-quadruplex formation using a thioflavin T (ThT) dye. This novel assay method is able to detect RNase H with a detection limit of 0.03 U /mL and further exhibits a good linearity R2 = 0.9923 at a concentration range of 0.03-1 U/mL under optimized conditions. Moreover, the inhibition effect of gentamycin on the RNase H activity is also studied. This strategy provides a potential tool for the biochemical enzyme analysis and inhibitor screening.
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Affiliation(s)
- Kefeng Wu
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China.
| | - Zhiyi Deng
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Ning Fang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Zhenwei Tang
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Xingxing Zhu
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410081, China
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13
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Zhang L, Yin X, Wang J, Xu D, Wang Y, Yang J, Tao Y, Zhang S, Feng X, Yan C. Associations between VDR Gene Polymorphisms and Osteoporosis Risk and Bone Mineral Density in Postmenopausal Women: A systematic review and Meta-Analysis. Sci Rep 2018; 8:981. [PMID: 29343720 PMCID: PMC5772668 DOI: 10.1038/s41598-017-18670-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 12/15/2017] [Indexed: 12/01/2022] Open
Abstract
Results on the relationships between vitamin D receptor (VDR) gene polymorphisms and postmenopausal osteoporosis (PMOP) susceptibility and bone mineral density (BMD) are conflicting. The aim of the study is to identify more eligible studies that calculated pooled OR and WMD with 95% CI to assess their associations. Overall, there were significant correlations between VDR ApaI, VDR FokI and PMOP susceptibility. Subgroup analysis showed that VDR ApaI polymorphism significantly decreased the osteoporosis risk in Caucasian postmenopausal women. In Asian populations, VDR BsmI and VDR FokI were associated with an increased risk of PMOP. As to the associations between VDR polymorphisms and BMD, Caucasian PMOP women carrying the ApaI aa genotype were at risk of high BMD in femoral neck, and low femoral neck BMD was observed in Caucasian PMOP women with FokI Ff genotype. PMOP women with the Cdx2 GA genotype had a lower lumbar spine BMD in overall and Caucasian populations compared with PMOP women with GG genotype. Different VDR gene polymorphisms have different impacts on PMOP risk and BMD.
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Affiliation(s)
- Liang Zhang
- Department of Orthopedics, Northern Jiangsu People's Hospital, Yangzhou, China
| | - Xin Yin
- Department of Orthopedics, First Affiliated Hospital of PLA General Hospital, Beijing, China
| | - Jingcheng Wang
- Department of Orthopedics, Northern Jiangsu People's Hospital, Yangzhou, China
| | - Daolinag Xu
- Department of Nephrology, Northern Jiangsu People's Hospital, Yangzhou, China
| | - Yongxiang Wang
- Department of Orthopedics, Northern Jiangsu People's Hospital, Yangzhou, China
| | - Jiandong Yang
- Department of Orthopedics, Northern Jiangsu People's Hospital, Yangzhou, China
| | - Yuping Tao
- Department of Orthopedics, Northern Jiangsu People's Hospital, Yangzhou, China
| | - Shengfei Zhang
- Department of Orthopedics, Northern Jiangsu People's Hospital, Yangzhou, China
| | - Xinmin Feng
- Department of Orthopedics, Northern Jiangsu People's Hospital, Yangzhou, China.
| | - Caifeng Yan
- Department of Endocrinology, Northern Jiangsu People's Hospital, Yangzhou, China.
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14
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Sasnauskas G, Tamulaitienė G, Tamulaitis G, Čalyševa J, Laime M, Rimšelienė R, Lubys A, Siksnys V. UbaLAI is a monomeric Type IIE restriction enzyme. Nucleic Acids Res 2017; 45:9583-9594. [PMID: 28934493 PMCID: PMC5766183 DOI: 10.1093/nar/gkx634] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/08/2017] [Accepted: 07/11/2017] [Indexed: 01/11/2023] Open
Abstract
Type II restriction endonucleases (REases) form a large and highly diverse group of enzymes. Even REases specific for a common recognition site often vary in their oligomeric structure, domain organization and DNA cleavage mechanisms. Here we report biochemical and structural characterization of the monomeric restriction endonuclease UbaLAI, specific for the pseudosymmetric DNA sequence 5'-CC/WGG-3' (where W = A/T, and '/' marks the cleavage position). We present a 1.6 Å co-crystal structure of UbaLAI N-terminal domain (UbaLAI-N) and show that it resembles the B3-family domain of EcoRII specific for the 5'-CCWGG-3' sequence. We also find that UbaLAI C-terminal domain (UbaLAI-C) is closely related to the monomeric REase MvaI, another enzyme specific for the 5'-CCWGG-3' sequence. Kinetic studies of UbaLAI revealed that it requires two recognition sites for optimal activity, and, like other type IIE enzymes, uses one copy of a recognition site to stimulate cleavage of a second copy. We propose that during the reaction UbaLAI-N acts as a handle that tethers the monomeric UbaLAI-C domain to the DNA, thereby helping UbaLAI-C to perform two sequential DNA nicking reactions on the second recognition site during a single DNA-binding event. A similar reaction mechanism may be characteristic to other monomeric two-domain REases.
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Affiliation(s)
- Giedrius Sasnauskas
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Giedrė Tamulaitienė
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Jelena Čalyševa
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Miglė Laime
- Thermo Fisher Scientific Baltics, V. A. Graiciuno str. 8, LT-02241, Vilnius, Lithuania
| | - Renata Rimšelienė
- Thermo Fisher Scientific Baltics, V. A. Graiciuno str. 8, LT-02241, Vilnius, Lithuania
| | - Arvydas Lubys
- Thermo Fisher Scientific Baltics, V. A. Graiciuno str. 8, LT-02241, Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
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15
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Tamulaitiene G, Jovaisaite V, Tamulaitis G, Songailiene I, Manakova E, Zaremba M, Grazulis S, Xu SY, Siksnys V. Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA. Nucleic Acids Res 2017; 45:3547-3558. [PMID: 28039325 PMCID: PMC5389614 DOI: 10.1093/nar/gkw1310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 01/19/2023] Open
Abstract
Although all Type II restriction endonucleases catalyze phosphodiester bond hydrolysis within or close to their DNA target sites, they form different oligomeric assemblies ranging from monomers, dimers, tetramers to higher order oligomers to generate a double strand break in DNA. Type IIP restriction endonuclease AgeI recognizes a palindromic sequence 5΄-A/CCGGT-3΄ and cuts it ('/' denotes the cleavage site) producing staggered DNA ends. Here, we present crystal structures of AgeI in apo and DNA-bound forms. The structure of AgeI is similar to the restriction enzymes that share in their target sites a conserved CCGG tetranucleotide and a cleavage pattern. Structure analysis and biochemical data indicate, that AgeI is a monomer in the apo-form both in the crystal and in solution, however, it binds and cleaves the palindromic target site as a dimer. DNA cleavage mechanism of AgeI is novel among Type IIP restriction endonucleases.
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Affiliation(s)
- Giedre Tamulaitiene
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Virginija Jovaisaite
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Inga Songailiene
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Elena Manakova
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Saulius Grazulis
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Shuang-yong Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
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16
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Havlicek S, Shen Y, Alpagu Y, Bruntraeger MB, Zufir NBM, Phuah ZY, Fu Z, Dunn NR, Stanton LW. Re-engineered RNA-Guided FokI-Nucleases for Improved Genome Editing in Human Cells. Mol Ther 2017; 25:342-355. [PMID: 28153087 PMCID: PMC5368403 DOI: 10.1016/j.ymthe.2016.11.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 11/07/2016] [Accepted: 11/07/2016] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 enables us to generate targeted sequence changes in the genomes of cells and organisms. However, off-target effects have been a persistent problem hampering the development of therapeutics based on CRISPR/Cas9 and potentially confounding research results. Efforts to improve Cas9 specificity, like the development of RNA-guided FokI-nucleases (RFNs), usually come at the cost of editing efficiency and/or genome targetability. To overcome these limitations, we engineered improved chimeras of RFNs that enable higher cleavage efficiency and provide broader genome targetability, while retaining high fidelity for genome editing in human cells. Furthermore, we developed a new RFN ortholog derived from Staphylococcus aureus Cas9 and characterize its utility for efficient genome engineering. Finally, we demonstrate the feasibility of RFN orthologs to functionally hetero-dimerize to modify endogenous genes, unveiling a new dimension of RFN target design opportunities.
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Affiliation(s)
- Steven Havlicek
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Yang Shen
- Bioinformatics Core, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Yunus Alpagu
- Endodermal Development and Differentiation Laboratory, Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Michaela B Bruntraeger
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Nurdiana B M Zufir
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Zhi Yi Phuah
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Zhiyan Fu
- Bioinformatics Core, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Norris R Dunn
- Endodermal Development and Differentiation Laboratory, Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Lawrence W Stanton
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 119077, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore.
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17
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Kulibaba RA, Liashenko YV, Yurko PS. [Not Available]. Tsitol Genet 2017; 51:76-77. [PMID: 30484611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A novel AluI-polymorphism in the fourth intron of chicken growth hormone gene was shown. It was detected the cytosine to thymine transition in the restriction site for AluI. Primers, that flanking the 460 bp fragment of the fourth intron, containing a polymorphic restriction site for AluI, was designed. The nucleotide sequence fragments amplified polymorphic variants was determined. Using designed primers was analyzed the genetic structure of populations of White Plymouth Rock, Poltava Clay, Rhode Island Red and Borkovskaya Barvistaya chicken breeds. It was found that growth hormone gene (by AluI-polymorphism in the fourthintron) was polymorphic in all experimental populations. Frequencies of alleles C and T in chicken population of White Plymouth Rock breed were 0,14 and 0,86; Rhode Island Red – 0,3 and 0,7; Poltava Clay – 0,04 and 0,96; Borkovskaya Barvistaya – 0,08 and 0,92 respectively. The tendency to increase egg production and egg weight of chicken with C/C genotype, as well as meat quality (live weight, carcass weight, weight of pectoral muscles) of chickens with genotype T/T of Rhode Island Red chicken breed was shown.
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18
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Alkhayal KA, Awadalia ZH, Vaali-Mohammed MA, Al Obeed OA, Al Wesaimer A, Halwani R, Zubaidi AM, Khan Z, Abdulla MH. Association of Vitamin D Receptor Gene Polymorphisms with Colorectal Cancer in a Saudi Arabian Population. PLoS One 2016; 11:e0155236. [PMID: 27309378 PMCID: PMC4911096 DOI: 10.1371/journal.pone.0155236] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/26/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Vitamin D, causally implicated in bone diseases and human malignancies, exerts its effects through binding to the vitamin D receptor (VDR). VDR is a transcription factor modulating the expression of several genes in different pathways. Genetic variants in the VDR gene have been associated with several cancers in different population including colorectal cancer. OBJECTIVE To assess the association of VDR gene polymorphisms in relation with colorectal cancer (CRC) in a Saudi population. METHODS The polymorphisms of VDR gene (BsmI, FokI, ApaI and TaqI) were analyzed by the polymerase chain reaction amplification of segments of interest followed by Sanger sequencing. One hundred diagnosed CRC patients and 100 healthy control subjects that were age and gender matched were recruited. RESULTS We did not observe significant association of any of the four VDR polymorphisms with colorectal cancer risk in the overall analysis. Although not statistically significant, the AA genotype of BsmI conferred about two-fold protection against CRCs compared to the GG genotype. Stratification of the study subjects based on age and gender suggests statistically significant association of CRC with the 'C' allele of ApaI in patients >57 years of age at disease diagnosis and BsmI polymorphism in females. In addition, statistically significant differences were observed for the genotypic distributions of VDR-BsmI, ApaI and TaqI SNPs between Saudi Arabian population and several of the International HapMap project populations. CONCLUSION Despite the absence of correlation of the examined VDR polymorphisms with CRCs in the combined analysis, ApaI and BsmI loci are statistically significantly associated with CRC in elderly and female patients, respectively. These findings need further validation in larger cohorts prior to utilizing these SNPs as potential screening markers for colorectal cancers in Saudi population.
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Affiliation(s)
- Khayal A. Alkhayal
- Colorectal Research Chair, Department of Surgery, King Khalid University hospital, College of medicine, King Saud University, Riyadh, Saudi Arabia
| | - Zainab H. Awadalia
- Colorectal Research Chair, Department of Surgery, King Khalid University hospital, College of medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mansoor-Ali Vaali-Mohammed
- Colorectal Research Chair, Department of Surgery, King Khalid University hospital, College of medicine, King Saud University, Riyadh, Saudi Arabia
| | - Omar A. Al Obeed
- Colorectal Research Chair, Department of Surgery, King Khalid University hospital, College of medicine, King Saud University, Riyadh, Saudi Arabia
| | - Alanoud Al Wesaimer
- Prince Sultan Military Medical City, Department of internal medicine, Riyadh, Saudi Arabia
| | - Rabih Halwani
- Prince Naif Center for Immunology Research and Asthma Research Chair, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed M. Zubaidi
- Colorectal Research Chair, Department of Surgery, King Khalid University hospital, College of medicine, King Saud University, Riyadh, Saudi Arabia
| | - Zahid Khan
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Maha-Hamadien Abdulla
- Colorectal Research Chair, Department of Surgery, King Khalid University hospital, College of medicine, King Saud University, Riyadh, Saudi Arabia
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Prieto J, Redondo P, Merino N, Villate M, Montoya G, Blanco FJ, Molina R. Structure of the I-SceI nuclease complexed with its dsDNA target and three catalytic metal ions. Acta Crystallogr F Struct Biol Commun 2016; 72:473-9. [PMID: 27303901 PMCID: PMC4909248 DOI: 10.1107/s2053230x16007512] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/04/2016] [Indexed: 01/22/2023] Open
Abstract
Homing endonucleases are highly specific DNA-cleaving enzymes that recognize and cleave long stretches of DNA. The engineering of these enzymes provides instruments for genome modification in a wide range of fields, including gene targeting. The homing endonuclease I-SceI from the yeast Saccharomyces cerevisiae has been purified after overexpression in Escherichia coli and its crystal structure has been determined in complex with its target DNA. In order to evaluate the number of ions that are involved in the cleavage process, thus determining the catalytic mechanism, crystallization experiments were performed in the presence of Mn(2+), yielding crystals that were suitable for X-ray diffraction analysis. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 80.11, b = 80.57, c = 130.87 Å, α = β = γ = 90°. The self-rotation function and the Matthews coefficient suggested the presence of two protein-DNA complexes in the asymmetric unit. The crystals diffracted to a resolution limit of 2.9 Å using synchrotron radiation. From the anomalous data, it was determined that three cations are involved in catalysis and it was confirmed that I-SceI follows a two-metal-ion DNA-strand cleavage mechanism.
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Affiliation(s)
- Jesús Prieto
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez Almagro 3, 28029 Madrid, Spain
| | - 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
- CIC bioGUNE, Parque Tecnológico de Vizcaya, Edificio 800, 48160 Derio, Spain
| | - Maider Villate
- CIC bioGUNE, Parque Tecnológico de Vizcaya, Edificio 800, 48160 Derio, 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
- Protein Structure and Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Francisco J. Blanco
- CIC bioGUNE, Parque Tecnológico de Vizcaya, Edificio 800, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation For Science, Alameda Urquijo 36-5, 48011 Bilbao, 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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Kmyta VV, Garbuzova VY, Prystupa EN, Prystupa LN. Bcl1 polymorphism of glucocorticoid receptor gene in patients with bronchial asthma with obesity. Tsitol Genet 2016; 50:36-41. [PMID: 30480407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The objective of this investigation was to analyze possible association between BclI polymorphism of glucocorticoid receptor gene and obesity in patients with bronchial asthma (BA). The study involved 188 patients with bronchial asthma and 95 apparently healthy adult individuals. Generally accepted assessments and examinations for BA diagnosis, and anthropometric, molecular-genetic and statistic methods of investigation were used in the research. It was found out that the patients with BA demonstrated higher body mass index (BMI) and higher ratio of fat centralization much more often, than the control group. Genotypes distribution for BclI polymorphism in patients with BA showed a statistically significant difference between patients with different BMI unlike the control group. Comparison of genotype frequency for BclI polymorphism in glucocorticoid receptor gene in individuals with different ratio of fat centralization in the control group and in the patients with BA separately showed statistically significant differences in the distribution of gene allelic variations only among the patients with BA. It was demonstrated that G/G genotype in the patients with visceral obesity was associated with BA.
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Callahan SJ, Luyten YA, Gupta YK, Wilson GG, Roberts RJ, Morgan RD, Aggarwal AK. Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities. PLoS Biol 2016; 14:e1002442. [PMID: 27082731 PMCID: PMC4833311 DOI: 10.1371/journal.pbio.1002442] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/17/2016] [Indexed: 01/18/2023] Open
Abstract
The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities has long been a goal of modern biology. The recently discovered Type IIL MmeI family of restriction-and-modification (RM) enzymes that possess a shared target recognition domain provides a framework for engineering such new specificities. However, a lack of structural information on Type IIL enzymes has limited the repertoire that can be rationally engineered. We report here a crystal structure of MmeI in complex with its DNA substrate and an S-adenosylmethionine analog (Sinefungin). The structure uncovers for the first time the interactions that underlie MmeI-DNA recognition and methylation (5’-TCCRAC-3’; R = purine) and provides a molecular basis for changing specificity at four of the six base pairs of the recognition sequence (5’-TCCRAC-3’). Surprisingly, the enzyme is resilient to specificity changes at the first position of the recognition sequence (5’-TCCRAC-3’). Collectively, the structure provides a basis for engineering further derivatives of MmeI and delineates which base pairs of the recognition sequence are more amenable to alterations than others. The structure of the bifunctional Type IIL restriction-and-modification enzyme MmeI provides a basis for understanding how such enzymes recognize their substrates and a framework for manipulating their specificities. Type II restriction endonucleases (REases) are the bedrock of modern biotechnology. Type II REases were essential for the recombinant DNA revolution and the development of gene technology. However, despite the discovery of more than 4,000 REases, the DNA recognition specificities are limited to only ~365. The recently discovered Type IIL MmeI family of restriction-and-modification (RM) enzymes provides a framework for understanding and engineering new specificities. We report here a crystal structure of MmeI in complex with its DNA substrate and an S-adenosylmethionine analog (Sinefungin). The structure uncovers for the first time the interactions that underlie MmeI-DNA recognition and methylation. The results establish a platform for rationally engineering further derivatives from MmeI and its homologs that will possess new, intentionally chosen, specificities.
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Affiliation(s)
- Scott J. Callahan
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Yvette A. Luyten
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Yogesh K. Gupta
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Geoffrey G. Wilson
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Richard J. Roberts
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Richard D. Morgan
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
- * E-mail: (RDM); (AKA)
| | - Aneel K. Aggarwal
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail: (RDM); (AKA)
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22
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Ziablitsev DS, Larin OS. Influence of single nucleotide polymorphisms of vitamin D receptor-gene on the level of osteoassociated hormones linkage with postmenopausal osteoporosis. ACTA ACUST UNITED AC 2016; 61:21-7. [PMID: 26845840 DOI: 10.15407/fz61.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The levels of osteoassociated hormones, macroelements, interleukines, cyclic nucleotides and activity of alkaline phosphatase were being detected in the blood plasma of 74 postmenopausal women with and without osteoporosis (OP). Bone mineral density (BMD) and the metacarpal index were being assessed according to the results of densitometry. The allele polymorphisms vitamin D receptor gene (VDR) Cdx2 (rs11568820) and TaqI (rs731236) were being identified with the help of the polymerase chain reaction. The major genotype CC TaqI was found in the group without OP 3.4 times more often than with OP, while the minor genotype TT was found 3.4 times more often with the presence of OP. The presence of the genotype CC TaqI decreased the risk of OP progress by 5.5 times, and the genotype TT TaqI increased by 5.4 times. The presence of the minor allele T was associated with the higher levels of interleukin 1β, BMD and lower testosterone blood level. The major homozygote AA Cdx2 was found in women without OP 2.9 times more often, while the minor genotype GG - 5.4 times more often with the presence of OP. The presence of the major homozygote decreased the risk of OP progress by more than 5.3 times, while the minor homozygote increased the risk by 8 times. The presence of the minor allele G in the genotype was associated with the increase of parathyroid hormone, phosphorus, magnesium, alkaline phosphatase activity in blood, BMD and with the decrease of testosterone, progesterone and calcium blood levels.
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Kurian P, Dunston G, Lindesay J. How quantum entanglement in DNA synchronizes double-strand breakage by type II restriction endonucleases. J Theor Biol 2016; 391:102-12. [PMID: 26682627 PMCID: PMC4746125 DOI: 10.1016/j.jtbi.2015.11.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 10/29/2015] [Accepted: 11/15/2015] [Indexed: 10/22/2022]
Abstract
Macroscopic quantum effects in living systems have been studied widely in pursuit of fundamental explanations for biological energy transport and sensing. While it is known that type II endonucleases, the largest class of restriction enzymes, induce DNA double-strand breaks by attacking phosphodiester bonds, the mechanism by which simultaneous cutting is coordinated between the catalytic centers remains unclear. We propose a quantum mechanical model for collective electronic behavior in the DNA helix, where dipole-dipole oscillations are quantized through boundary conditions imposed by the enzyme. Zero-point modes of coherent oscillations would provide the energy required for double-strand breakage. Such quanta may be preserved in the presence of thermal noise by the enzyme's displacement of water surrounding the DNA recognition sequence. The enzyme thus serves as a decoherence shield. Palindromic mirror symmetry of the enzyme-DNA complex should conserve parity, because symmetric bond-breaking ceases when the symmetry of the complex is violated or when physiological parameters are perturbed from optima. Persistent correlations in DNA across longer spatial separations-a possible signature of quantum entanglement-may be explained by such a mechanism.
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Affiliation(s)
- P Kurian
- National Human Genome Center, Howard University College of Medicine, Washington, DC 20059, USA; Department of Physics and Astronomy, Howard University, Washington, DC 20059, USA; Computational Physics Laboratory, Howard University, Washington, DC 20059, USA.
| | - G Dunston
- National Human Genome Center, Howard University College of Medicine, Washington, DC 20059, USA; Department of Microbiology, Howard University College of Medicine, Washington, DC 20059, USA
| | - J Lindesay
- Department of Physics and Astronomy, Howard University, Washington, DC 20059, USA; Computational Physics Laboratory, Howard University, Washington, DC 20059, USA
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Prystupa L, Savchenko O, Koroza S. [ASSOCIATION OF CYCLIC CITRULLINATED PEPTIDE ANTIBODIES LEVEL WITH RHEUMATOID ARTHRITIS ACTIVITY BASED ON GLUCOCORTICOID RECEPTOR GENE BBL1 POLYMORPHISM]. Georgian Med News 2015:44-48. [PMID: 26483373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The ambiguity of facts on connection between glucocorticoid receptor gene (GR) Bcl1 polymorphism in rheumatoid arthritis (RA) and its activity as well as lack of facts on its association with serological variants of the desease, makes ir reasonable to investigate its connections between cyclic citrullinated peptide antibodiss (ACCP) concentration and clinico-laboratorial parameters of RA (DAS 28 desease activity score, C-reactive protein concentration (CRP) and erythrocyte sedimentation rate (ESR) level based on GR gene Bcl1 polymorphism. Study involved 161 RA patients aged over 40 as well as 96 healthy individuals. Routine examination of RA diagnostics, anthropometric and molecular genetic methods were used in the research. Statistical analysis of the results was performed using SPSS-17 program. It has been proved that there is no significant difference in GR gene Bcl1 polymorphism distribution based on DAS 28 RA desease activity score, ACCP concentration and ESR level. However, we have found out that G/G genotype bearers have positive correlation relationship between ACCP titre and RA activity by laboratorial parameters (CRP, ESR),DAS 28 score and rheumatoid factor (RF) which has not been found in C/C and C/G genotype bearing patients. The above indicates the association of G/G genotype by GR gene Bcl1 polymorphism with clinico-laboratorial parameters of RA inflammatory activity. In course of the study we have identified the existance of correlation relationship between ACCP concentration and DAS 28 score of RA activity, CRP concentration and ESR level in individuals bearing G/G gene by GR gene Bcl11 polymorphism gene. The association between GR gene Bcl1 polymorphism and clinico-laboratorial parameters of RA inflammatory activity has not been found.
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MESH Headings
- Adult
- Aged
- Anti-Citrullinated Protein Antibodies/blood
- Arthritis, Rheumatoid/blood
- Arthritis, Rheumatoid/genetics
- Arthritis, Rheumatoid/immunology
- Arthritis, Rheumatoid/physiopathology
- Blood Sedimentation
- C-Reactive Protein/genetics
- C-Reactive Protein/immunology
- Case-Control Studies
- Deoxyribonucleases, Type II Site-Specific/chemistry
- Female
- Gene Expression
- Genotype
- Humans
- Male
- Middle Aged
- Peptides, Cyclic/blood
- Peptides, Cyclic/immunology
- Polymorphism, Restriction Fragment Length
- Receptors, Glucocorticoid/genetics
- Receptors, Glucocorticoid/immunology
- Rheumatoid Factor/genetics
- Rheumatoid Factor/immunology
- Severity of Illness Index
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Affiliation(s)
- L Prystupa
- Sumy State University, Medical Institute, Department of Internal Medicine, Ukraine
| | - O Savchenko
- Sumy State University, Medical Institute, Department of Internal Medicine, Ukraine
| | - S Koroza
- Sumy State University, Medical Institute, Department of Internal Medicine, Ukraine
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25
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Aouida M, Eid A, Ali Z, Cradick T, Lee C, Deshmukh H, Atef A, AbuSamra D, Gadhoum SZ, Merzaban J, Bao G, Mahfouz M. Efficient fdCas9 Synthetic Endonuclease with Improved Specificity for Precise Genome Engineering. PLoS One 2015; 10:e0133373. [PMID: 26225561 PMCID: PMC4520497 DOI: 10.1371/journal.pone.0133373] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 06/25/2015] [Indexed: 12/26/2022] Open
Abstract
The Cas9 endonuclease is used for genome editing applications in diverse eukaryotic species. A high frequency of off-target activity has been reported in many cell types, limiting its applications to genome engineering, especially in genomic medicine. Here, we generated a synthetic chimeric protein between the catalytic domain of the FokI endonuclease and the catalytically inactive Cas9 protein (fdCas9). A pair of guide RNAs (gRNAs) that bind to sense and antisense strands with a defined spacer sequence range can be used to form a catalytically active dimeric fdCas9 protein and generate double-strand breaks (DSBs) within the spacer sequence. Our data demonstrate an improved catalytic activity of the fdCas9 endonuclease, with a spacer range of 15-39 nucleotides, on surrogate reporters and genomic targets. Furthermore, we observed no detectable fdCas9 activity at known Cas9 off-target sites. Taken together, our data suggest that the fdCas9 endonuclease variant is a superior platform for genome editing applications in eukaryotic systems including mammalian cells.
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Affiliation(s)
- Mustapha Aouida
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Thomas Cradick
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, United States of America
| | - Ciaran Lee
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, United States of America
| | - Harshavardhan Deshmukh
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, United States of America
| | - Ahmed Atef
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Dina AbuSamra
- Laboratory of Cell Signaling and Migration, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Samah Zeineb Gadhoum
- Laboratory of Cell Signaling and Migration, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Jasmeen Merzaban
- Laboratory of Cell Signaling and Migration, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, United States of America
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
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26
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Shah S, Sanchez J, Stewart A, Piperakis MM, Cosstick R, Nichols C, Park CK, Ma X, Wysocki V, Bitinaite J, Horton NC. Probing the run-on oligomer of activated SgrAI bound to DNA. PLoS One 2015; 10:e0124783. [PMID: 25880668 PMCID: PMC4399878 DOI: 10.1371/journal.pone.0124783] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 03/05/2015] [Indexed: 02/04/2023] Open
Abstract
SgrAI is a type II restriction endonuclease with an unusual mechanism of activation involving run-on oligomerization. The run-on oligomer is formed from complexes of SgrAI bound to DNA containing its 8 bp primary recognition sequence (uncleaved or cleaved), and also binds (and thereby activates for DNA cleavage) complexes of SgrAI bound to secondary site DNA sequences which contain a single base substitution in either the 1st/8th or the 2nd/7th position of the primary recognition sequence. This modulation of enzyme activity via run-on oligomerization is a newly appreciated phenomenon that has been shown for a small but increasing number of enzymes. One outstanding question regarding the mechanistic model for SgrAI is whether or not the activating primary site DNA must be cleaved by SgrAI prior to inducing activation. Herein we show that an uncleavable primary site DNA containing a 3'-S-phosphorothiolate is in fact able to induce activation. In addition, we now show that cleavage of secondary site DNA can be activated to nearly the same degree as primary, provided a sufficient number of flanking base pairs are present. We also show differences in activation and cleavage of the two types of secondary site, and that effects of selected single site substitutions in SgrAI, as well as measured collisional cross-sections from previous work, are consistent with the cryo-electron microscopy model for the run-on activated oligomer of SgrAI bound to DNA.
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Affiliation(s)
- Santosh Shah
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Jonathan Sanchez
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Andrew Stewart
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
- Genetics Graduate Program, University of Arizona, Tucson, AZ 85721, United States of America
| | - Michael M. Piperakis
- Department of Chemistry, University of Liverpool, Liverpool, United Kingdom, L69 7ZD, United States of America
| | - Richard Cosstick
- Department of Chemistry, University of Liverpool, Liverpool, United Kingdom, L69 7ZD, United States of America
| | - Claire Nichols
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Chad K. Park
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Xin Ma
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, United States of America
| | - Vicki Wysocki
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, United States of America
| | - Jurate Bitinaite
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, United States of America
| | - Nancy C. Horton
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
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27
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Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases--a historical perspective and more. Nucleic Acids Res 2014; 42:7489-527. [PMID: 24878924 PMCID: PMC4081073 DOI: 10.1093/nar/gku447] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/02/2014] [Accepted: 05/07/2014] [Indexed: 12/17/2022] Open
Abstract
This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.
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Affiliation(s)
- Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Geoffrey G Wilson
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA
| | - Wolfgang Wende
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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28
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Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol 2014; 32:569-76. [PMID: 24770325 PMCID: PMC4090141 DOI: 10.1038/nbt.2908] [Citation(s) in RCA: 704] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/16/2014] [Indexed: 12/26/2022]
Abstract
Monomeric CRISPR-Cas9 nucleases are widely used for targeted genome editing but can induce unwanted off-target mutations with high frequencies. Here we describe dimeric RNA-guided FokI nucleases (RFNs) that can recognize extended sequences and edit endogenous genes with high efficiencies in human cells. RFN cleavage activity depends strictly on the binding of two guide RNAs (gRNAs) to DNA with a defined spacing and orientation substantially reducing the likelihood that a suitable target site will occur more than once in the genome and therefore improving specificities relative to wild-type Cas9 monomers. RFNs guided by a single gRNA generally induce lower levels of unwanted mutations than matched monomeric Cas9 nickases. In addition, we describe a simple method for expressing multiple gRNAs bearing any 5' end nucleotide, which gives dimeric RFNs a broad targeting range. RFNs combine the ease of RNA-based targeting with the specificity enhancement inherent to dimerization and are likely to be useful in applications that require highly precise genome editing.
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Affiliation(s)
- Shengdar Q Tsai
- 1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [2] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [4] Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicolas Wyvekens
- 1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [2] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Cyd Khayter
- 1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [2] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Jennifer A Foden
- 1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [2] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Vishal Thapar
- 1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [2] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Deepak Reyon
- 1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [2] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [4] Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mathew J Goodwin
- 1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [2] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Martin J Aryee
- 1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [2] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - J Keith Joung
- 1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [2] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [4] Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
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Smith MW, Ghindilis AL, Seoudi IA, Smith K, Billharz R, Simon HM. A new restriction endonuclease-based method for highly-specific detection of DNA targets from methicillin-resistant Staphylococcus aureus. PLoS One 2014; 9:e97826. [PMID: 24831802 PMCID: PMC4022673 DOI: 10.1371/journal.pone.0097826] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022] Open
Abstract
PCR multiplexing has proven to be challenging, and thus has provided limited means for pathogen genotyping. We developed a new approach for analysis of PCR amplicons based on restriction endonuclease digestion. The first stage of the restriction enzyme assay is hybridization of a target DNA to immobilized complementary oligonucleotide probes that carry a molecular marker, horseradish peroxidase (HRP). At the second stage, a target-specific restriction enzyme is added, cleaving the target-probe duplex at the corresponding restriction site and releasing the HRP marker into solution, where it is quantified colorimetrically. The assay was tested for detection of the methicillin-resistant Staphylococcus aureus (MRSA) pathogen, using the mecA gene as a target. Calibration curves indicated that the limit of detection for both target oligonucleotide and PCR amplicon was approximately 1 nM. Sequences of target oligonucleotides were altered to demonstrate that (i) any mutation of the restriction site reduced the signal to zero; (ii) double and triple point mutations of sequences flanking the restriction site reduced restriction to 50–80% of the positive control; and (iii) a minimum of a 16-bp target-probe dsDNA hybrid was required for significant cleavage. Further experiments showed that the assay could detect the mecA amplicon from an unpurified PCR mixture with detection limits similar to those with standard fluorescence-based qPCR. Furthermore, addition of a large excess of heterologous genomic DNA did not affect amplicon detection. Specificity of the assay is very high because it involves two biorecognition steps. The proposed assay is low-cost and can be completed in less than 1 hour. Thus, we have demonstrated an efficient new approach for pathogen detection and amplicon genotyping in conjunction with various end-point and qPCR applications. The restriction enzyme assay may also be used for parallel analysis of multiple different amplicons from the same unpurified mixture in broad-range PCR applications.
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Affiliation(s)
- Maria W. Smith
- Center for Coastal Margin Observation & Prediction, and Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon, United States of America
- Cascade Biosystems, Inc., Colfax, Wisconsin, United States of America
- * E-mail:
| | | | | | - Kenneth Smith
- Cascade Biosystems, Inc., Colfax, Wisconsin, United States of America
| | - Rosalind Billharz
- Pacific Lutheran University, Department of Biology, Tacoma, Washington, United States of America
| | - Holly M. Simon
- Center for Coastal Margin Observation & Prediction, and Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon, United States of America
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30
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Xu T, Yu H, Xu P, Xu W, Chen W, Chen C, Li X. Real-time enzyme-digesting identification of double-strand DNA in a resonance-cantilever embedded micro-chamber. Lab Chip 2014; 14:1206-1214. [PMID: 24496267 DOI: 10.1039/c3lc51294k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A novel direct identification of double-strand DNA is proposed by using real-time enzyme-digestion in a resonant-cantilever embedded microfluidic chip. The new gene-level detection method is expected to replace the conventional DNA-hybridization based gene-detection that suffers from not only nonspecific adsorption induced false-positives but also complicated single-strand DNA preparation and hybridization. Since a detected DNA chain features a unique cutting site for a certain restriction-enzyme, the accurately cut-off mass (representing the length of the digested segment) can be online recorded by the frequency-shift signal of the resonant micro-cantilever sensor. This enzyme-digestion technique is confirmed by experimental identification of the stx2 gene of E. coli O157:H7. The direct-PCR sample is directly analyzed by using our lab-made cantilever-embedded microfluidic-chip. The 3776 bp DNA is immobilized via biotin-streptavidin binding and the added mass is recorded by a frequency-decrease of 15.9 kHz within 10 min. Then, with EcoRV-enzyme digestion at the site of 2635 bp, the cut-off mass is real-time detected by a frequency-increase of 10.2 kHz within 6 min. The detected frequency-shift ratio of 15.9/10.2 = 64.2% is consistent with the length ratio between the cut-off fragment and the whole DNA chain (2635/3776 = 69.8%). Hence, the simple and accurate double-strand detection method is verified experimentally.
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Affiliation(s)
- Tiegang Xu
- State Key Lab of Transducer Technology and Science and Technology on Microsystem Lab, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.
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Lampropoulos A, Sutikovic Z, Wenzl C, Maegele I, Lohmann JU, Forner J. GreenGate---a novel, versatile, and efficient cloning system for plant transgenesis. PLoS One 2013; 8:e83043. [PMID: 24376629 PMCID: PMC3869738 DOI: 10.1371/journal.pone.0083043] [Citation(s) in RCA: 263] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 11/08/2013] [Indexed: 12/02/2022] Open
Abstract
Building expression constructs for transgenesis is one of the fundamental day-to-day tasks in modern biology. Traditionally it is based on a multitude of type II restriction endonucleases and T4 DNA ligase. Especially in case of long inserts and applications requiring high-throughput, this approach is limited by the number of available unique restriction sites and the need for designing individual cloning strategies for each project. Several alternative cloning systems have been developed in recent years to overcome these issues, including the type IIS enzyme based Golden Gate technique. Here we introduce our GreenGate system for rapidly assembling plant transformation constructs, which is based on the Golden Gate method. GreenGate cloning is simple and efficient since it uses only one type IIS restriction endonuclease, depends on only six types of insert modules (plant promoter, N-terminal tag, coding sequence, C-terminal tag, plant terminator and plant resistance cassette), but at the same time allows assembling several expression cassettes in one binary destination vector from a collection of pre-cloned building blocks. The system is cheap and reliable and when combined with a library of modules considerably speeds up cloning and transgene stacking for plant transformation.
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Affiliation(s)
- Athanasios Lampropoulos
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Zoran Sutikovic
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Christian Wenzl
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Ira Maegele
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Jan U. Lohmann
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Joachim Forner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
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Lyumkis D, Talley H, Stewart A, Shah S, Park CK, Tama F, Potter CS, Carragher B, Horton NC. Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. Structure 2013; 21:1848-58. [PMID: 24055317 PMCID: PMC3898938 DOI: 10.1016/j.str.2013.08.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 10/26/2022]
Abstract
SgrAI is a sequence specific DNA endonuclease that functions through an unusual enzymatic mechanism that is allosterically activated 200- to 500-fold by effector DNA, with a concomitant expansion of its DNA sequence specificity. Using single-particle transmission electron microscopy to reconstruct distinct populations of SgrAI oligomers, we show that in the presence of allosteric, activating DNA, the enzyme forms regular, repeating helical structures characterized by the addition of DNA-binding dimeric SgrAI subunits in a run-on manner. We also present the structure of oligomeric SgrAI at 8.6 Å resolution, demonstrating the conformational state of SgrAI in its activated form. Activated and oligomeric SgrAI displays key protein-protein interactions near the helix axis between its N termini, as well as allosteric protein-DNA interactions that are required for enzymatic activation. The hybrid approach reveals an unusual mechanism of enzyme activation that explains SgrAI's oligomerization and allosteric behavior.
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Affiliation(s)
- Dmitry Lyumkis
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Heather Talley
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Andrew Stewart
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
- Genetics Interdisciplinary Graduate Program, University of Arizona, Tucson, AZ, 85721
| | - Santosh Shah
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Chad K. Park
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Florence Tama
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Clinton S. Potter
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Nancy C. Horton
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
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Richter S, Morrison S, Connor T, Su J, Print CG, Ronimus RS, McGee SL, Wilson WR. Zinc finger nuclease mediated knockout of ADP-dependent glucokinase in cancer cell lines: effects on cell survival and mitochondrial oxidative metabolism. PLoS One 2013; 8:e65267. [PMID: 23799003 PMCID: PMC3683018 DOI: 10.1371/journal.pone.0065267] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 04/23/2013] [Indexed: 01/22/2023] Open
Abstract
Zinc finger nucleases (ZFN) are powerful tools for editing genes in cells. Here we use ZFNs to interrogate the biological function of ADPGK, which encodes an ADP-dependent glucokinase (ADPGK), in human tumour cell lines. The hypothesis we tested is that ADPGK utilises ADP to phosphorylate glucose under conditions where ATP becomes limiting, such as hypoxia. We characterised two ZFN knockout clones in each of two lines (H460 and HCT116). All four clones had frameshift mutations in all alleles at the target site in exon 1 of ADPGK, and were ADPGK-null by immunoblotting. ADPGK knockout had little or no effect on cell proliferation, but compromised the ability of H460 cells to survive siRNA silencing of hexokinase-2 under oxic conditions, with clonogenic survival falling from 21±3% for the parental line to 6.4±0.8% (p = 0.002) and 4.3±0.8% (p = 0.001) for the two knockouts. A similar increased sensitivity to clonogenic cell killing was observed under anoxia. No such changes were found when ADPGK was knocked out in HCT116 cells, for which the parental line was less sensitive than H460 to anoxia and to hexokinase-2 silencing. While knockout of ADPGK in HCT116 cells caused few changes in global gene expression, knockout of ADPGK in H460 cells caused notable up-regulation of mRNAs encoding cell adhesion proteins. Surprisingly, we could discern no consistent effect on glycolysis as measured by glucose consumption or lactate formation under anoxia, or extracellular acidification rate (Seahorse XF analyser) under oxic conditions in a variety of media. However, oxygen consumption rates were generally lower in the ADPGK knockouts, in some cases markedly so. Collectively, the results demonstrate that ADPGK can contribute to tumour cell survival under conditions of high glycolytic dependence, but the phenotype resulting from knockout of ADPGK is cell line dependent and appears to be unrelated to priming of glycolysis in these lines.
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Affiliation(s)
- Susan Richter
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
| | - Shona Morrison
- Metabolic Research Unit, School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Tim Connor
- Metabolic Research Unit, School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Jiechuang Su
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
| | - Cristin G. Print
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Bioinformatics Institute, The University of Auckland, Auckland, New Zealand
| | | | - Sean L. McGee
- Metabolic Research Unit, School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - William R. Wilson
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
- * E-mail:
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Abstract
Although many approaches based on template replication were developed and applied in DNA detection, cross-contamination from amplicons is always a vexing problem. Thus, signal amplification is preferable for DNA detection due to its low risk of cross-contamination from amplicons. Here, we proposed a cascade enzymatic signal amplification (termed as CESA) by coupling Afu flap endonuclease with nicking endonuclease, including three steps: invasive signal amplification, flap ligation, and nicking endonuclease signal amplification. Because of the advantages of low risk of contamination, no sequence requirement of target DNA, and the universal reaction conditions for any target detection, CESA has a great potential in clinical diagnosis.
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Affiliation(s)
- Bingjie Zou
- Department of Pharmacology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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Marozik P, Mosse I, Alekna V, Rudenko E, Tamulaitienė M, Ramanau H, Strazdienė V, Samokhovec V, Ameliyanovich M, Byshnev N, Gonchar A, Kundas L, Zhur K. Association Between Polymorphisms of VDR, COL1A1, and LCT genes and bone mineral density in Belarusian women with severe postmenopausal osteoporosis. Medicina (Kaunas) 2013; 49:177-184. [PMID: 23985982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
BACKGROUND AND OBJECTIVE. Variation of osteoporosis in the population is the result of an interaction between the genotype and the environment, and the genetic causes of osteoporosis are being widely investigated. The aim of this study was to analyze the association between the polymorphisms of the vitamin D receptor (VDR), type I collagen (COL1A1), and lactase (LCT) genes and severe postmenopausal osteoporosis as well as bone mineral density (BMD). MATERIAL AND METHODS. A total of 54 women with severe postmenopausal osteoporosis and 77 controls (mean age, 58.3 years [SD, 6.2] and 56.7 years [SD, 7.42], respectively) were included into the study. The subjects were recruited at the City Center for Osteoporosis Prevention (Minsk, Belarus). Dual-energy x-ray absorptiometry was used to measure bone mineral density at the lumbar spine and the femoral neck. Severe osteoporosis was diagnosed in the women with the clinical diagnosis of postmenopausal osteoporosis and at least 1 fragility fracture. The control group included women without osteoporosis. Polymorphic sites in osteoporosis predisposition genes (ApaI, BsmI, TaqI, and Cdx2 of the VDR gene, G2046T of the COL1A1 gene, and T-13910C of the LCT gene) were determined using the polymerase chain reaction on the deoxyribonucleic acid isolated from dried bloodspots. RESULTS. The data showed that the ApaI and BsmI polymorphisms of the VDR gene and T- 13910C of the LCT gene were associated with severe postmenopausal osteoporosis in the analyzed Belarusian women (P<0.01). A statistically significant positive correlation between the VDR risk genotypes ApaI and TaqI and bone mineral density was found (P<0.05). CONCLUSIONS. The findings of this study suggest that at least the ApaI and BsmI polymorphisms of the VDR gene and T-13910C of the LCT gene are associated with the risk of postmenopausal osteoporosis in our sample of the Belarusian women.
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Affiliation(s)
- Pavel Marozik
- Institute of Genetics and Cytology NAS Belarus, Belarus
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Kusar D, Kavalic M, Ocepek M, Zdovc I. Report on overcoming the poor quality of Apai pulsotypes with a short review on PFGE for listeria monocytogenes. Pol J Microbiol 2013; 62:307-309. [PMID: 24459838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
Since listeriosis, caused by Listeria monocytogenes, is one of the important concerns of public health in Europe related to foodborne zoonoses, an efficient protocol for isolate typing is necessary when performing epidemiological studies. Three standardized PFGE protocols available for L. monocytogenes were briefly reviewed. Since observing a poor-quality of ApaI pulsotypes in our laboratory, enzymes from three different manufacturers were compared. The obtained pulsotypes showed that restriction digestion with ApaI from New England BioLabs should be complemented with a subsequent overnight incubation of PFGE plugs in TE buffer for better performance.
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Affiliation(s)
- Darja Kusar
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Maja Kavalic
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Matjaz Ocepek
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
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Podgórska B, Kujawska G, Skurzewski M, Batsko O, Kaczorowski T. A rapid and simple method for detection of type II restriction endonucleases in cells of bacteria with high activity of nonspecific nucleases. Acta Biochim Pol 2012; 59:669-672. [PMID: 23130356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/16/2012] [Accepted: 10/29/2012] [Indexed: 06/01/2023]
Abstract
In this work we describe a novel, rapid and simple microscale procedure for identification of restriction endonuclease activity in bacteria lysates, which contain high levels of non-specific DNA nucleases.
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Affiliation(s)
- Beata Podgórska
- Department of Molecular Evolution, University of Gdańsk, Gdańsk, Poland
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Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.
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Affiliation(s)
- Martin Jinek
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Krzysztof Chylinski
- Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| | - Ines Fonfara
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| | - Michael Hauer
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Present address: Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Jennifer A. Doudna
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Emmanuelle Charpentier
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
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Zaremba M, Sasnauskas G, Siksnys V. The link between restriction endonuclease fidelity and oligomeric state: a study with Bse634I. FEBS Lett 2012; 586:3324-9. [PMID: 22828280 DOI: 10.1016/j.febslet.2012.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 07/02/2012] [Accepted: 07/06/2012] [Indexed: 11/18/2022]
Abstract
Type II restriction endonucleases (REases) exist in multiple oligomeric forms. The tetrameric REases have two DNA binding interfaces and must synapse two recognition sites to achieve cleavage. It was hypothesised that binding of two recognition sites by tetrameric enzymes contributes to their fidelity. Here, we experimentally determined the fidelity for Bse634I REase in different oligomeric states. Surprisingly, we find that tetramerisation does not increase REase fidelity in comparison to the dimeric variant. Instead, an inherent ability to act concertedly at two sites provides tetrameric REase with a safety-catch to prevent host DNA cleavage if a single unmodified site becomes available.
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40
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Schierling B, Dannemann N, Gabsalilow L, Wende W, Cathomen T, Pingoud A. A novel zinc-finger nuclease platform with a sequence-specific cleavage module. Nucleic Acids Res 2012; 40:2623-38. [PMID: 22135304 PMCID: PMC3315325 DOI: 10.1093/nar/gkr1112] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 11/04/2011] [Accepted: 11/06/2011] [Indexed: 12/18/2022] Open
Abstract
Zinc-finger nucleases (ZFNs) typically consist of three to four zinc fingers (ZFs) and the non-specific DNA-cleavage domain of the restriction endonuclease FokI. In this configuration, the ZFs constitute the binding module and the FokI domain the cleavage module. Whereas new binding modules, e.g. TALE sequences, have been considered as alternatives to ZFs, no efforts have been undertaken so far to replace the catalytic domain of FokI as the cleavage module in ZFNs. Here, we have fused a three ZF array to the restriction endonuclease PvuII to generate an alternative ZFN. While PvuII adds an extra element of specificity when combined with ZFs, ZF-PvuII constructs must be designed such that only PvuII sites with adjacent ZF-binding sites are cleaved. To achieve this, we introduced amino acid substitutions into PvuII that alter K(m) and k(cat) and increase fidelity. The optimized ZF-PvuII fusion constructs cleave DNA at addressed sites with a >1000-fold preference over unaddressed PvuII sites in vitro as well as in cellula. In contrast to the 'analogous' ZF-FokI nucleases, neither excess of enzyme over substrate nor prolonged incubation times induced unaddressed cleavage in vitro. These results present the ZF-PvuII platform as a valid alternative to conventional ZFNs.
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Affiliation(s)
- Benno Schierling
- Institute of Biochemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany.
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Abstract
It has been proposed that certain type II restriction enzymes (REs), such as EcoRV, track the helical pitch of DNA as they diffuse along DNA, a so-called rotation-coupled sliding. As of yet, there is no direct experimental observation of this phenomenon, but mounting indirect evidence gained from single-molecule imaging of RE-DNA complexes support the hypothesis. We address this issue by conjugating fluorescent labels of varying size (organic dyes, proteins and quantum dots) to EcoRV, and by fusing it to the engineered Rop protein scRM6. Single-molecule imaging of these modified EcoRVs sliding along DNA provides us with their linear diffusion constant (D(1)), revealing a significant size dependency. To account for the dependence of D(1) on the size of the EcoRV label, we have developed four theoretical models describing different types of motion along DNA and find that our experimental results are best described by rotation-coupled sliding of the protein. The similarity of EcoRV to other type II REs and DNA binding proteins suggests that this type of motion could be widely preserved in other biological contexts.
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Affiliation(s)
- Jasmina Dikić
- Laboratoire Kastler Brossel, ENS, UPMC-Paris6, CNRS UMR 8552, 24 rue Lhomond, 75005 Paris, France.
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Abstract
Here we present a protocol for generating transgenic embryos in Xenopus using I-SceI meganuclease. This method relies on integration of DNA constructs, containing one or two I-SceI meganuclease sites. It is a simpler method than the REMI method of transgenesis, and it is ideally suited for generating transgenic lines in Xenopus laevis and Xenopus tropicalis. In addition to it being simpler than the REMI method, this protocol also results in single copy integration events rather than tandem concatemers. Although the protocol we describe is for X. tropicalis, the method can also be used to generate transgenic lines in X. laevis. We also describe a convenient method for designing and generating complex constructs for transgenesis, named pTransgenesis, based on the Multisite Gateway(®) cloning, which include I-SceI sites and Tol2 elements to facilitate genome integration.
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Affiliation(s)
- Shoko Ishibashi
- The Healing Foundation Centre, The Faculty of Life Sciences, University of Manchester, Manchester, England, UK
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Gogas Yavuz D, Keskin L, Kıyıcı S, Sert M, Yazıcı D, Şahin İ, Yüksel M, Deyneli O, Aydın H, Tuncel E, Akalın S. Vitamin D receptor gene BsmI, FokI, ApaI, TaqI polymorphisms and bone mineral density in a group of Turkish type 1 diabetic patients. Acta Diabetol 2011; 48:329-336. [PMID: 21538164 DOI: 10.1007/s00592-011-0284-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 04/09/2011] [Indexed: 01/02/2023]
Abstract
Previous studies have suggested an influence of vitamin D receptor alleles on bone metabolism and on susceptibility to type 1 diabetes mellitus in different ethnic populations. We aimed to investigate the distribution of vitamin D receptor (VDR) alleles in relation to biochemical bone turnover parameters and bone densitometry measurements in a group of Turkish type 1 diabetic patients. One hundred and seventeen patients (M/F 57/60, 27.6 ± 7.3 y duration of diabetes 8.1 ± 6.3 y) and 134 healthy controls (M/F 61/73, 26.2 ± 5.3 y) were included in the study. Bone mineral density (BMD) was evaluated by dual-energy X-ray absorptiometry (DEXA). The vitamin D receptor gene (VDR) polymorphisms FokI, Bsm1, Apa1, and Taq1 were examined using a PCR-based restriction analysis. Serum levels of calcium, phosphor osteocalcin, intact parathyroid hormone, and C telopeptide were measured. Vitamin D receptor Bsm1 Fok1, Apa1, and Taq1 genotype distributions were not different between patient with diabetes and control groups. BMD was 0.77 ± 0.2 g/cm(2) vs. 0.97 ± 0.2 g/cm(2) (P = 0.0001) for the femur, 1.0 ± 0.1 g/cm(2) vs. 1.13 ± 0.1 g/cm(2) (P = 0.001) for type 1 diabetic patients and controls. Bone turnover markers were significantly lower in type 1 diabetic group. BMD measurements and bone metabolic markers were not different between the genotypes in either the patient with diabetes or the controls. The VDR gene polymorphisms, Bsm1, Fok 1, Apa1, and Taq1 showed no influence on bone metabolism in our group of type 1 diabetic patients.
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Affiliation(s)
- Dilek Gogas Yavuz
- Section of Endocrinology and Metabolism, Marmara University School of Medicine, Tibbiye caddesi. No: 49 Haydarpasa, Istanbul, Turkey.
| | - Lezan Keskin
- Section of Endocrinology and Metabolism, Inonu University Medical School, Malatya, Turkey
| | - Sinem Kıyıcı
- Section of Endocrinology and Metabolism, Uludağ University Medical School, Bursa, Turkey
| | - Murat Sert
- Section of Endocrinology and Metabolism, Cukurova University Medical School, Adana, Turkey
| | - Dilek Yazıcı
- Section of Endocrinology and Metabolism, Marmara University School of Medicine, Tibbiye caddesi. No: 49 Haydarpasa, Istanbul, Turkey
| | - İbrahim Şahin
- Section of Endocrinology and Metabolism, Inonu University Medical School, Malatya, Turkey
| | - Meral Yüksel
- Marmara University Vocational School of Health, Istanbul, Turkey
| | - Oğuzhan Deyneli
- Section of Endocrinology and Metabolism, Marmara University School of Medicine, Tibbiye caddesi. No: 49 Haydarpasa, Istanbul, Turkey
| | - Hasan Aydın
- Section of Endocrinology and Metabolism, Marmara University School of Medicine, Tibbiye caddesi. No: 49 Haydarpasa, Istanbul, Turkey
| | - Ercan Tuncel
- Section of Endocrinology and Metabolism, Uludağ University Medical School, Bursa, Turkey
| | - Sema Akalın
- Section of Endocrinology and Metabolism, Marmara University School of Medicine, Tibbiye caddesi. No: 49 Haydarpasa, Istanbul, Turkey
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Callahan SJ, Morgan RD, Jain R, Townson SA, Wilson GG, Roberts RJ, Aggarwal AK. Crystallization and preliminary crystallographic analysis of the type IIL restriction enzyme MmeI in complex with DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1262-5. [PMID: 22102043 PMCID: PMC3212378 DOI: 10.1107/s1744309111028041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/13/2011] [Indexed: 11/10/2022]
Abstract
Type IIL restriction enzymes have rejuvenated the search for user-specified DNA binding and cutting. By aligning and contrasting the highly comparable amino-acid sequences yet diverse recognition specificities across the family of enzymes, amino acids involved in DNA binding have been identified and mutated to produce alternative binding specificities. To date, the specificity of MmeI (a type IIL restriction enzyme) has successfully been altered at positions 3, 4 and 6 of the asymmetric TCCRAC (where R is a purine) DNA-recognition sequence. To further understand the structural basis of MmeI DNA-binding specificity, the enzyme has been crystallized in complex with its DNA substrate. The crystal belonged to space group P1, with unit-cell parameters a = 61.73, b = 94.96, c = 161.24 Å, α = 72.79, β = 89.12, γ = 71.68°, and diffracted to 2.6 Å resolution when exposed to synchrotron radiation. The structure promises to reveal the basis of MmeI DNA-binding specificity and will complement efforts to create enzymes with novel specificities.
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Affiliation(s)
- Scott J. Callahan
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, New York, NY 10029-6574, USA
| | | | - Rinku Jain
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, New York, NY 10029-6574, USA
| | - Sharon A. Townson
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, New York, NY 10029-6574, USA
| | | | | | - Aneel K. Aggarwal
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, New York, NY 10029-6574, USA
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Li T, Huang S, Zhao X, Wright DA, Carpenter S, Spalding MH, Weeks DP, Yang B. Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Res 2011; 39:6315-25. [PMID: 21459844 PMCID: PMC3152341 DOI: 10.1093/nar/gkr188] [Citation(s) in RCA: 314] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Revised: 03/16/2011] [Accepted: 03/16/2011] [Indexed: 12/29/2022] Open
Abstract
Recent studies indicate that the DNA recognition domain of transcription activator-like (TAL) effectors can be combined with the nuclease domain of FokI restriction enzyme to produce TAL effector nucleases (TALENs) that, in pairs, bind adjacent DNA target sites and produce double-strand breaks between the target sequences, stimulating non-homologous end-joining and homologous recombination. Here, we exploit the four prevalent TAL repeats and their DNA recognition cipher to develop a 'modular assembly' method for rapid production of designer TALENs (dTALENs) that recognize unique DNA sequence up to 23 bases in any gene. We have used this approach to engineer 10 dTALENs to target specific loci in native yeast chromosomal genes. All dTALENs produced high rates of site-specific gene disruptions and created strains with expected mutant phenotypes. Moreover, dTALENs stimulated high rates (up to 34%) of gene replacement by homologous recombination. Finally, dTALENs caused no detectable cytotoxicity and minimal levels of undesired genetic mutations in the treated yeast strains. These studies expand the realm of verified TALEN activity from cultured human cells to an intact eukaryotic organism and suggest that low-cost, highly dependable dTALENs can assume a significant role for gene modifications of value in human and animal health, agriculture and industry.
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Affiliation(s)
- Ting Li
- Department of Genetics, Development and Cell Biology, Laurence H. Baker Center for Bioinformatics and Biological Statistics, Department of Animal Science, Iowa State University, Ames, IA 50011 and Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Sheng Huang
- Department of Genetics, Development and Cell Biology, Laurence H. Baker Center for Bioinformatics and Biological Statistics, Department of Animal Science, Iowa State University, Ames, IA 50011 and Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Xuefeng Zhao
- Department of Genetics, Development and Cell Biology, Laurence H. Baker Center for Bioinformatics and Biological Statistics, Department of Animal Science, Iowa State University, Ames, IA 50011 and Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David A. Wright
- Department of Genetics, Development and Cell Biology, Laurence H. Baker Center for Bioinformatics and Biological Statistics, Department of Animal Science, Iowa State University, Ames, IA 50011 and Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Susan Carpenter
- Department of Genetics, Development and Cell Biology, Laurence H. Baker Center for Bioinformatics and Biological Statistics, Department of Animal Science, Iowa State University, Ames, IA 50011 and Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Martin H. Spalding
- Department of Genetics, Development and Cell Biology, Laurence H. Baker Center for Bioinformatics and Biological Statistics, Department of Animal Science, Iowa State University, Ames, IA 50011 and Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Donald P. Weeks
- Department of Genetics, Development and Cell Biology, Laurence H. Baker Center for Bioinformatics and Biological Statistics, Department of Animal Science, Iowa State University, Ames, IA 50011 and Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Bing Yang
- Department of Genetics, Development and Cell Biology, Laurence H. Baker Center for Bioinformatics and Biological Statistics, Department of Animal Science, Iowa State University, Ames, IA 50011 and Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
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Spasskaia DS, Karpov DS, Karpov VL. [Escherichia coli Dam methylase as a molecular tool for mapping binding sites of the yeast transcription factor Rpn4]. Mol Biol (Mosk) 2011; 45:642-651. [PMID: 21954596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Rpn4p is a transcription factor responsible for coordinated regulation of proteasomal genes in Saccharomyces cerevisiae. This factor is involved directly or indirectly in regulation of comprise more than one tenth part of all yeast genome. Traditional methods are inappropriate for mapping of Rpn4p binding sites because of its extremely low concentration in the cell. We have developed the model system using Dam-methylase of E. coli which allows to detect interaction of Rpn4p with its target genes. In this system we showed that Rpn4p is recruited to proteasomal genes only through interactions with DNA.
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Bonnet I, Desbiolles P. The diffusion constant of a labeled protein sliding along DNA. Eur Phys J E Soft Matter 2011; 34:25. [PMID: 21400049 DOI: 10.1140/epje/i2011-11025-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 02/11/2011] [Indexed: 05/30/2023]
Abstract
Long ago inferred by biochemists, the linear diffusion of proteins along DNA has recently been observed at a single-molecule level using fluorescence microscopy. This imaging technique requires labeling the protein of interest with a fluorophore, usually an organic nanosized dye that is not supposed to impact the dynamics of the protein. Yet individual proteins can also be tracked using much larger labels, like quantum dots or beads. We investigate here the impact of such a large label on the protein diffusion along DNA. Solving a Fokker-Planck equation, we estimate the diffusion constant of a protein-label complex diffusing in a periodic potential that mimics the DNA-protein interaction, the link between the protein and the label being modeled as a Hookean spring. Our results indicate that the diffusion constant can generally be calculated by considering that the motion of the protein in the DNA potential is decoupled from the Brownian motion of the label. Our conclusions are in good agreement with the experimental results we obtained with the restriction enzyme EcoRV, assuming a rotation-coupled diffusion of the enzyme along DNA.
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Affiliation(s)
- I Bonnet
- Laboratoire Kastler Brossel, ENS, UPMC-Paris, CNRS UMR, France
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48
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Mokrishcheva ML, Solonin AS, Nikitin DV. Fused eco29kIR- and M genes coding for a fully functional hybrid polypeptide as a model of molecular evolution of restriction-modification systems. BMC Evol Biol 2011; 11:35. [PMID: 21291520 PMCID: PMC3039593 DOI: 10.1186/1471-2148-11-35] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 02/03/2011] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The discovery of restriction endonucleases and modification DNA methyltransferases, key instruments of genetic engineering, opened a new era of molecular biology through development of the recombinant DNA technology. Today, the number of potential proteins assigned to type II restriction enzymes alone is beyond 6000, which probably reflects the high diversity of evolutionary pathways. Here we present experimental evidence that a new type IIC restriction and modification enzymes carrying both activities in a single polypeptide could result from fusion of the appropriate genes from preexisting bipartite restriction-modification systems. RESULTS Fusion of eco29kIR and M ORFs gave a novel gene encoding for a fully functional hybrid polypeptide that carried both restriction endonuclease and DNA methyltransferase activities. It has been placed into a subclass of type II restriction and modification enzymes--type IIC. Its MTase activity, 80% that of the M.Eco29kI enzyme, remained almost unchanged, while its REase activity decreased by three times, concurrently with changed reaction optima, which presumably can be caused by increased steric hindrance in interaction with the substrate. In vitro the enzyme preferentially cuts DNA, with only a low level of DNA modification detected. In vivo new RMS can provide a 102-fold less protection of host cells against phage invasion. CONCLUSIONS We propose a molecular mechanism of appearing of type IIC restriction-modification and M.SsoII-related enzymes, as well as other multifunctional proteins. As shown, gene fusion could play an important role in evolution of restriction-modification systems and be responsible for the enzyme subclass interconversion. Based on the proposed approach, hundreds of new type IIC enzymes can be generated using head-to-tail oriented type I, II, and III restriction and modification genes. These bifunctional polypeptides can serve a basis for enzymes with altered recognition specificities. Lastly, this study demonstrates that protein fusion may change biochemical properties of the involved enzymes, thus giving a starting point for their further evolutionary divergence.
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Affiliation(s)
- Marina L Mokrishcheva
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, Pushchino, Moscow region 142290, Russia
- Pushchino State University, Prospekt Nauki, 3, Pushchino, Moscow region 142290, Russia
| | - Alexander S Solonin
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, Pushchino, Moscow region 142290, Russia
| | - Dmitri V Nikitin
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, Pushchino, Moscow region 142290, Russia
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Little EJ, Dunten PW, Bitinaite J, Horton NC. New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA. Acta Crystallogr D Biol Crystallogr 2011; 67:67-74. [PMID: 21206063 PMCID: PMC3016018 DOI: 10.1107/s0907444910047785] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 11/17/2010] [Indexed: 11/10/2022]
Abstract
SgrAI is a type II restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-activation with expansion of DNA-sequence specificity. The three-dimensional crystal structures of SgrAI bound to cleaved primary-site DNA and Mg²(+) and bound to secondary-site DNA with either Mg²(+) or Ca²(+) are presented. All three structures show a conformation of enzyme and DNA similar to the previously determined dimeric structure of SgrAI bound to uncleaved primary-site DNA and Ca²(+) [Dunten et al. (2008), Nucleic Acids Res. 36, 5405-5416], with the exception of the cleaved bond and a slight shifting of the DNA in the SgrAI/cleaved primary-site DNA/Mg²(+) structure. In addition, a new metal ion binding site is located in one of the two active sites in this structure, which is consistent with proposals for the existence of a metal-ion site near the 3'-O leaving group.
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Affiliation(s)
- Elizabeth J. Little
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Pete W. Dunten
- Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | | | - Nancy C. Horton
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
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Gupta A, Meng X, Zhu LJ, Lawson ND, Wolfe SA. Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res 2011; 39:381-92. [PMID: 20843781 PMCID: PMC3017618 DOI: 10.1093/nar/gkq787] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 08/16/2010] [Accepted: 08/19/2010] [Indexed: 01/12/2023] Open
Abstract
Zinc finger nucleases (ZFNs) facilitate tailor-made genomic modifications in vivo through the creation of targeted double-stranded breaks. They have been employed to modify the genomes of plants and animals, and cell-based therapies utilizing ZFNs are undergoing clinical trials. However, many ZFNs display dose-dependent toxicity presumably due to the generation of undesired double-stranded breaks at off-target sites. To evaluate the parameters influencing the functional specificity of ZFNs, we compared the in vivo activity of ZFN variants targeting the zebrafish kdrl locus, which display both high on-target activity and dose-dependent toxicity. We evaluated their functional specificity by assessing lesion frequency at 141 potential off-target sites using Illumina sequencing. Only a minority of these off-target sites accumulated lesions, where the thermodynamics of zinc finger-DNA recognition appear to be a defining feature of active sites. Surprisingly, we observed that both the specificity of the incorporated zinc fingers and the choice of the engineered nuclease domain could independently influence the fidelity of these ZFNs. The results of this study have implications for the assessment of likely off-target sites within a genome and point to both zinc finger-dependent and -independent characteristics that can be tailored to create ZFNs with greater precision.
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Affiliation(s)
- Ankit Gupta
- Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Xiangdong Meng
- Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lihua J. Zhu
- Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nathan D. Lawson
- Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Scot A. Wolfe
- Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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