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Liu Y, Kong J, Liu G, Li Z, Xiao Y. Precise Gene Knock-In Tools with Minimized Risk of DSBs: A Trend for Gene Manipulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401797. [PMID: 38728624 PMCID: PMC11267366 DOI: 10.1002/advs.202401797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Gene knock-in refers to the insertion of exogenous functional genes into a target genome to achieve continuous expression. Currently, most knock-in tools are based on site-directed nucleases, which can induce double-strand breaks (DSBs) at the target, following which the designed donors carrying functional genes can be inserted via the endogenous gene repair pathway. The size of donor genes is limited by the characteristics of gene repair, and the DSBs induce risks like genotoxicity. New generation tools, such as prime editing, transposase, and integrase, can insert larger gene fragments while minimizing or eliminating the risk of DSBs, opening new avenues in the development of animal models and gene therapy. However, the elimination of off-target events and the production of delivery carriers with precise requirements remain challenging, restricting the application of the current knock-in treatments to mainly in vitro settings. Here, a comprehensive review of the knock-in tools that do not/minimally rely on DSBs and use other mechanisms is provided. Moreover, the challenges and recent advances of in vivo knock-in treatments in terms of the therapeutic process is discussed. Collectively, the new generation of DSBs-minimizing and large-fragment knock-in tools has revolutionized the field of gene editing, from basic research to clinical treatment.
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Affiliation(s)
- Yongfeng Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Mudi Meng Honors CollegeChina Pharmaceutical UniversityNanjing210009China
| | - Jianping Kong
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Gongyu Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Zhaoxing Li
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
| | - Yibei Xiao
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
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2
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Zfhx4 regulates endochondral ossification as the transcriptional platform of Osterix in mice. Commun Biol 2021; 4:1258. [PMID: 34732852 PMCID: PMC8566502 DOI: 10.1038/s42003-021-02793-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 10/18/2021] [Indexed: 11/08/2022] Open
Abstract
Endochondral ossification is regulated by transcription factors that include SRY-box transcription factor 9, runt-related protein 2 (Runx2), and Osterix. However, the sequential and harmonious regulation of the multiple steps of endochondral ossification is unclear. This study identified zinc finger homeodomain 4 (Zfhx4) as a crucial transcriptional partner of Osterix. We found that Zfhx4 was highly expressed in cartilage and that Zfhx4 deficient mice had reduced expression of matrix metallopeptidase 13 and inhibited calcification of cartilage matrices. These phenotypes were very similar to impaired chondrogenesis in Osterix deficient mice. Coimmunoprecipitation and immunofluorescence indicated a physical interaction between Zfhx4 and Osterix. Notably, Zfhx4 and Osterix double mutant mice showed more severe phenotype than Zfhx4 deficient mice. Additionally, Zfhx4 interacted with Runx2 that functions upstream of Osterix. Our findings suggest that Zfhx4 coordinates the transcriptional network of Osterix and, consequently, endochondral ossification.
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3
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Chao G, Travis C, Church G. Measurement of large serine integrase enzymatic characteristics in HEK293 cells reveals variability and influence on downstream reporter expression. FEBS J 2021; 288:6410-6427. [PMID: 34043859 DOI: 10.1111/febs.16037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/20/2021] [Accepted: 05/25/2021] [Indexed: 11/30/2022]
Abstract
Large serine integrases (LSIs) offer tremendous potential for rapid genetic engineering as well as building biological systems capable of responding to stimuli and integrating information. Currently, there is no unified metric for directly measuring the enzymatic characteristics of LSI function, which hinders evaluation of their suitability to specific applications. Here, we present an experimental protocol for recording DNA recombination in HEK293 cells in real-time through fluorophore expression and software which fits the kinetic data to a model tailored to LSI recombination dynamics. Our model captures the activity of LSIs as three parameters: expression level (Kexp ), catalytic rate (kcat ), and substrate affinity (Kd ). The expression level and catalytic rate for phiC31 and Bxb1 varied greatly, suggesting disparate routes to high recombination efficiencies. Moreover, the expression level and substrate affinity jointly impacted downstream reporter expression, potentially by obstructing transcriptional machinery. We validated these observations by swapping between promoters and mutating key recombinase residues and DNA recognition sites to individually modulate each parameter. Our model for identifying key LSI parameters in cellulo provides insight into selecting the optimal recombinase for various applications as well as for guiding the engineering of improved LSIs.
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Affiliation(s)
- George Chao
- Genetics Department, Harvard Medical School, Boston, MA, USA
| | - Clair Travis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George Church
- Genetics Department, Harvard Medical School, Boston, MA, USA
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4
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Kvasko AY, Isayenkov SV, Dmytruk KV, Sibirny AA, Blume YB, Yemets AI. Obtaining Wheat (Triticum aestivum L.) Lines with Yeast Genes for Trehalose Biosynthesis. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720040088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Gao H, Qi X, Hart DJ, Gao S, Wang H, Xu S, Zhang Y, Liu X, Liu Y, An Y. Three Novel Escherichia coli Vectors for Convenient and Efficient Molecular Biological Manipulations. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6123-6131. [PMID: 29798665 DOI: 10.1021/acs.jafc.8b01960] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We have constructed novel plasmids pANY2, pANY3, and pANY6 for flexible cloning with low false positives, efficient expression, and convenient purification of proteins. The pANY2 plasmid can be used for efficient isopropyl-β-d-thiogalactoside (IPTG) induced protein expression, while the pANY3 plasmid can be used for temperature-induced expression. The pANY6 plasmid contains a self-cleaving elastin-like protein (ELP) tag for purification of recombinant protein by simple ELP-mediated precipitation steps and removal of the ELP tag by self-cleavage. A urea-based denaturation and refolding processes for renaturation of insoluble inclusion bodies can be conveniently integrated into the ELP-mediated precipitation protocol, removing time-consuming dialysis steps. These novel vectors, together with the described strategies of gene cloning, protein expression, and purification, may have wide applications in biosciences, agricultural, food technologies, and so forth.
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Affiliation(s)
- Herui Gao
- College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang 110161 , China
| | - Xianghui Qi
- School of Food and Biological Engineering , Jiangsu University , Zhenjiang 212013 , China
| | - Darren J Hart
- Institut de Biologie Structurale (IBS), CEA, CNRS , University Grenoble Alpes , Grenoble 38044 , France
| | - Song Gao
- College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang 110161 , China
| | - Hongling Wang
- College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang 110161 , China
| | - Shumin Xu
- College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang 110161 , China
| | - Yifeng Zhang
- College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang 110161 , China
| | - Xia Liu
- College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang 110161 , China
| | - Yifei Liu
- College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang 110161 , China
| | - Yingfeng An
- College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang 110161 , China
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6
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Liu X, Li T, Hart DJ, Gao S, Wang H, Gao H, Xu S, Zhang Y, Liu Y, An Y. A universal mini-vector and an annealing of PCR products (APP)-based cloning strategy for convenient molecular biological manipulations. Biochem Biophys Res Commun 2018; 497:978-982. [PMID: 29448102 DOI: 10.1016/j.bbrc.2018.02.099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 02/07/2018] [Accepted: 02/09/2018] [Indexed: 12/23/2022]
Abstract
Currently, the most widely used strategies for molecular cloning are sticky-end ligation-based cloning, TA cloning, blunt-end ligation-based cloning and ligase-independent cloning. In this study we have developed a novel mini-vector pANY1 which can simultaneously meet the requirements of all these cloning strategies. In addition, the selection of appropriate restriction digestion sites is difficult in some cases because of the presence of internal sites. In this study, an annealing of PCR products (APP)-based sticky-end cloning strategy was introduced to avoid this issue. Additionally, false positives occur during molecular cloning, which increases the workload of isolating positive clones. The plasmid pANY1 contains a ccdB cassette between multiple cloning sites, which efficiently avoids these false positives. Therefore, this mini-vector should serve as a useful tool with wide applications in biosciences, agriculture, food technologies, etc.
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Affiliation(s)
- Xia Liu
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Tuoping Li
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Darren J Hart
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble 38044, France
| | - Song Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Hongling Wang
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China; College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Herui Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Shumin Xu
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yifeng Zhang
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yifei Liu
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yingfeng An
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China.
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7
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CagL from Helicobacter pylori has ADP-ribosylation activity and exerts partial protective efficacy in mice. Arch Biochem Biophys 2017; 635:102-109. [DOI: 10.1016/j.abb.2017.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/20/2017] [Accepted: 10/26/2017] [Indexed: 12/26/2022]
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8
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Konczal J, Gray CH. Streamlining workflow and automation to accelerate laboratory scale protein production. Protein Expr Purif 2017; 133:160-169. [PMID: 28330825 DOI: 10.1016/j.pep.2017.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/17/2017] [Indexed: 12/20/2022]
Abstract
Protein production facilities are often required to produce diverse arrays of proteins for demanding methodologies including crystallography, NMR, ITC and other reagent intensive techniques. It is common for these teams to find themselves a bottleneck in the pipeline of ambitious projects. This pressure to deliver has resulted in the evolution of many novel methods to increase capacity and throughput at all stages in the pipeline for generation of recombinant proteins. This review aims to describe current and emerging options to accelerate the success of protein production in Escherichia coli. We emphasize technologies that have been evaluated and implemented in our laboratory, including innovative molecular biology and expression vectors, small-scale expression screening strategies and the automation of parallel and multidimensional chromatography.
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Affiliation(s)
- Jennifer Konczal
- Drug Discovery Program, CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, United Kingdom
| | - Christopher H Gray
- Drug Discovery Program, CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, United Kingdom.
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9
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Shi Z, Vickers CE. Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects. Metab Eng Commun 2016; 3:173-186. [PMID: 29468123 PMCID: PMC5779711 DOI: 10.1016/j.meteno.2016.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 03/30/2016] [Accepted: 05/10/2016] [Indexed: 01/15/2023] Open
Abstract
Molecular Cloning Designer Simulator (MCDS) is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1) it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2) it can perform a user-defined workflow of cloning steps in a single execution of the software; (3) it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4) it includes experimental information to conveniently guide wet lab work; and (5) it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com. MCDS is an all-in-one in silico design, simulation and management platform. MCDS supports the design, simulation management of most cloning and recombineering technologies. MCDS has a novel interactive flowchart that allows simpler and more precise transactions. MCDS enables complete information integrity and consistency by keeping all details in one file.
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Affiliation(s)
- Zhenyu Shi
- Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Claudia E Vickers
- Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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10
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High-throughput cloning, expression and purification of glycoside hydrolases using Ligation-Independent Cloning (LIC). Protein Expr Purif 2014; 99:35-42. [DOI: 10.1016/j.pep.2014.03.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/25/2014] [Accepted: 03/15/2014] [Indexed: 12/21/2022]
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11
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Fogg PCM, Colloms S, Rosser S, Stark M, Smith MCM. New applications for phage integrases. J Mol Biol 2014; 426:2703-16. [PMID: 24857859 PMCID: PMC4111918 DOI: 10.1016/j.jmb.2014.05.014] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 11/28/2022]
Abstract
Within the last 25 years, bacteriophage integrases have rapidly risen to prominence as genetic tools for a wide range of applications from basic cloning to genome engineering. Serine integrases such as that from ϕC31 and its relatives have found an especially wide range of applications within diverse micro-organisms right through to multi-cellular eukaryotes. Here, we review the mechanisms of the two major families of integrases, the tyrosine and serine integrases, and the advantages and disadvantages of each type as they are applied in genome engineering and synthetic biology. In particular, we focus on the new areas of metabolic pathway construction and optimization, biocomputing, heterologous expression and multiplexed assembly techniques. Integrases are versatile and efficient tools that can be used in conjunction with the various extant molecular biology tools to streamline the synthetic biology production line. Phage integrases are site-specific recombinases that mediate controlled and precise DNA integration and excision. The serine integrases, such as ϕC31 integrase, can be used for efficient recombination in heterologous hosts as they use short recombination substrates, they are directional and they do not require host factors. Both serine and tyrosine integrases, such as λ integrase, are versatile tools for DNA cloning and assembly in vivo and in vitro. Controlled expression of orthologous serine integrases and their cognate recombination directionality factors can be used to generate living biocomputers. Serine integrases are increasingly being exploited for synthetic biology applications.
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Affiliation(s)
- Paul C M Fogg
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Sean Colloms
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Susan Rosser
- School of Biological Sciences, University of Edinburgh, King's Building, Edinburgh EH9 3JR, UK
| | - Marshall Stark
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Margaret C M Smith
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
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12
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Biopharmaceutical protein production bySaccharomyces cerevisiae: current state and future prospects. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Zheng J, Rubin EJ, Bifani P, Mathys V, Lim V, Au M, Jang J, Nam J, Dick T, Walker JR, Pethe K, Camacho LR. para-Aminosalicylic acid is a prodrug targeting dihydrofolate reductase in Mycobacterium tuberculosis. J Biol Chem 2013; 288:23447-56. [PMID: 23779105 DOI: 10.1074/jbc.m113.475798] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
para-Aminosalicylic acid (PAS) is one of the antimycobacterial drugs currently used for multidrug-resistant tuberculosis. Although it has been in clinical use for over 60 years, its mechanism(s) of action remains elusive. Here we report that PAS is a prodrug targeting dihydrofolate reductase (DHFR) through an unusual and novel mechanism of action. We provide evidences that PAS is incorporated into the folate pathway by dihydropteroate synthase (DHPS) and dihydrofolate synthase (DHFS) to generate a hydroxyl dihydrofolate antimetabolite, which in turn inhibits DHFR enzymatic activity. Interestingly, PAS is recognized by DHPS as efficiently as its natural substrate para-amino benzoic acid. Chemical inhibition of DHPS or mutation in DHFS prevents the formation of the antimetabolite, thereby conferring resistance to PAS. In addition, we identified a bifunctional enzyme (riboflavin biosynthesis protein (RibD)), a putative functional analog of DHFR in a knock-out strain. This finding is further supported by the identification of PAS-resistant clinical isolates encoding a RibD overexpression mutation displaying cross-resistance to genuine DHFR inhibitors. Our findings reveal that a metabolite of PAS inhibits DHFR in the folate pathway. RibD was shown to act as a functional analog of DHFR, and as for DHFS, both were shown to be associated in PAS resistance in laboratory strains and clinical isolates.
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Affiliation(s)
- Jun Zheng
- Novartis Institute for Tropical Diseases, Singapore 138670.
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14
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Yan X, Shen Y. Preliminary crystallographic analysis of the kinase domain of SAD-1, a protein essential for presynaptic differentiation in Caenorhabditis elegans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:449-52. [PMID: 23545657 PMCID: PMC3614176 DOI: 10.1107/s1744309113006088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/04/2013] [Indexed: 11/11/2022]
Abstract
SAD-1 is a serine/threonine kinase which plays an important role in the regulation of both neuronal polarity and synapse formation in Caenorhabditis elegans. The kinase domain of SAD-1 from C. elegans was overexpressed in Escherichia coli BL21 (DE3) cells and purified to homogeneity using nickel-nitrilotriacetic acid metal-affinity, ion-exchange and gel-filtration chromatography. Diffraction-quality crystals were grown using the sitting-drop vapour-diffusion technique from a condition consisting of 1 M CAPSO pH 9.6, 10%(w/v) polyethylene glycol 3350. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 205.4, b = 57.1, c = 71.7 Å, β = 106.1°. X-ray diffraction data were recorded to 3.0 Å resolution from a single crystal using synchrotron radiation.
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Affiliation(s)
- Xiaojie Yan
- Department of BMB, Basic Medical College, Tianjin Medical University, Tianjin 300070, People's Republic of China.
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15
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HDL-like discs for assaying membrane proteins in drug discovery. Biophys Chem 2012; 165-166:56-61. [DOI: 10.1016/j.bpc.2012.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 03/09/2012] [Indexed: 01/03/2023]
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16
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Radulovich N, Leung L, Tsao MS. Modified gateway system for double shRNA expression and Cre/lox based gene expression. BMC Biotechnol 2011; 11:24. [PMID: 21418658 PMCID: PMC3070635 DOI: 10.1186/1472-6750-11-24] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 03/22/2011] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The growing need for functional studies of genes has set the stage for the development of versatile tools for genetic manipulations. RESULTS Aiming to provide tools for high throughput analysis of gene functions, we have developed a modified short hairpin RNA (shRNA) and gene expression system based on Gateway Technology. The system contains a series of entry and destination vectors that enables easy transfer of shRNA or cDNA into lentiviral expression systems with a variety of selection or marker genes (i.e. puromycin, hygromycin, green fluorescent protein-EGFP, yellow fluorescent protein-YFP and red fluorescent protein-dsRed2). Our shRNA entry vector pENTR.hU6.hH1 containing two tandem human shRNA expression promoters, H1 and U6, was capable of co-expressing two shRNA sequences simultaneously. The entry vector for gene overexpression, pENTR.CMV.ON was constructed to contain CMV promoter with a multiple cloning site flanked by loxP sites allowing for subsequent Cre/lox recombination. Both shRNA and cDNA expression vectors also contained attL sites necessary for recombination with attR sites in our destination expression vectors. As proof of principle we demonstrate the functionality and efficiency of this system by testing expression of several cDNA and shRNA sequences in a number of cell lines. CONCLUSION Our system is a valuable addition to already existing library of Gateway based vectors and can be an essential tool for many aspects of gene functional studies.
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Affiliation(s)
- Nikolina Radulovich
- University Health Network, Ontario Cancer Institute/Princess Margaret Hospital Site, 610 University Ave., Toronto, Ontario, M5G 2M9, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Medical Sciences Buildings, 1 King's College Circle, Toronto, Ontario, M5 S 1A8, Canada
| | - Lisa Leung
- University Health Network, Ontario Cancer Institute/Princess Margaret Hospital Site, 610 University Ave., Toronto, Ontario, M5G 2M9, Canada
- Department of Medical Biophysics, University Health Network, Ontario Cancer Institute/Princess Margaret Hospital Site, 610 University Ave., Toronto, Ontario, M5G 2M9, Canada
| | - Ming-Sound Tsao
- University Health Network, Ontario Cancer Institute/Princess Margaret Hospital Site, 610 University Ave., Toronto, Ontario, M5G 2M9, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Medical Sciences Buildings, 1 King's College Circle, Toronto, Ontario, M5 S 1A8, Canada
- Department of Medical Biophysics, University Health Network, Ontario Cancer Institute/Princess Margaret Hospital Site, 610 University Ave., Toronto, Ontario, M5G 2M9, Canada
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Identification of mammalian protein complexes by lentiviral-based affinity purification and mass spectrometry. Methods Mol Biol 2011; 781:31-45. [PMID: 21877275 DOI: 10.1007/978-1-61779-276-2_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein complexes and protein-protein interactions (PPIs) are fundamental for most biological functions. Deciphering the extensive protein interaction networks that occur within cellular contexts has become a logical extension to the human genome project. Proteome-scale interactome analysis of mammalian systems requires efficient methods for accurately detecting PPIs with specific considerations for the intrinsic technical challenges of mammalian genome manipulation. In this chapter, we outline in detail an innovative lentiviral-based functional proteomic approach that can be used to rapidly characterize protein complexes from a broad range of mammalian cell lines. This method integrates the following key features: (1) lentiviral elements for efficient delivery of tagged constructs into mammalian cell lines; (2) site-specific Gateway™ recombination sites for easy cloning; (3) versatile epitope-tagging system for flexible affinity purification strategies; and (4) LC-MS-based protein identification using tandem mass spectrometry.
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18
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Pearlstein RA, Hu QY, Zhou J, Yowe D, Levell J, Dale B, Kaushik VK, Daniels D, Hanrahan S, Sherman W, Abel R. New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: analysis of the epidermal growth factor-like repeat A docking site using WaterMap. Proteins 2010; 78:2571-86. [PMID: 20589640 DOI: 10.1002/prot.22767] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
LDL cholesterol (LDL-C) is cleared from plasma via cellular uptake and internalization processes that are largely mediated by the low-density lipoprotein cholesterol receptor (LDL-R). LDL-R is targeted for lysosomal degradation by association with proprotein convertase subtilisin-kexin type 9 (PCSK9). Gain of function mutations in PCSK9 can result in excessive loss of receptors and dyslipidemia. On the other hand, receptor-sparing phenomena, including loss-of-function mutations or inhibition of PCSK9, can lead to enhanced clearance of plasma lipids. We hypothesize that desolvation and resolvation processes, in many cases, constitute rate-determining steps for protein-ligand association and dissociation, respectively. To test this hypothesis, we analyzed and compared the predicted desolvation properties of wild-type versus gain-of-function mutant Asp374Tyr PCSK9 using WaterMap, a new in silico method for predicting the preferred locations and thermodynamic properties of water solvating proteins ("hydration sites"). We compared these results with binding kinetics data for PCSK9, full-length LDL-R ectodomain, and isolated EGF-A repeat. We propose that the fast k(on) and entropically driven thermodynamics observed for PCSK9-EGF-A binding stem from the functional replacement of water occupying stable PCSK9 hydration sites (i.e., exchange of PCSK9 H-bonds from water to polar EGF-A groups). We further propose that the relatively fast k(off) observed for EGF-A unbinding stems from the limited displacement of solvent occupying unstable hydration sites. Conversely, the slower k(off) observed for EGF-A and LDL-R unbinding from Asp374Tyr PCSK9 stems from the destabilizing effects of this mutation on PCSK9 hydration sites, with a concomitant increase in the persistence of the bound complex.
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Affiliation(s)
- Robert A Pearlstein
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, Cambridge, Massachusetts 02139, USA.
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The structure of Ca2+ sensor Case16 reveals the mechanism of reaction to low Ca2+ concentrations. SENSORS 2010; 10:8143-60. [PMID: 22163646 PMCID: PMC3231237 DOI: 10.3390/s100908143] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 07/28/2010] [Accepted: 08/12/2010] [Indexed: 12/11/2022]
Abstract
Here we report the first crystal structure of a high-contrast genetically encoded circularly permuted green fluorescent protein (cpGFP)-based Ca2+ sensor, Case16, in the presence of a low Ca2+ concentration. The structure reveals the positioning of the chromophore within Case16 at the first stage of the Ca2+-dependent response when only two out of four Ca2+-binding pockets of calmodulin (CaM) are occupied with Ca2+ ions. In such a “half Ca2+-bound state”, Case16 is characterized by an incomplete interaction between its CaM-/M13-domains. We also report the crystal structure of the related Ca2+ sensor Case12 at saturating Ca2+ concentration. Based on this structure, we postulate that cpGFP-based Ca2+ sensors can form non-functional homodimers where the CaM-domain of one sensor molecule binds symmetrically to the M13-peptide of the partner sensor molecule. Case12 and Case16 behavior upon addition of high concentrations of free CaM or M13-peptide reveals that the latter effectively blocks the fluorescent response of the sensor. We speculate that the demonstrated intermolecular interaction with endogenous substrates and homodimerization can impede proper functioning of this type of Ca2+ sensors in living cells.
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Reliable fusion PCR mediated by GC-rich overlap sequences. Gene 2009; 434:43-9. [DOI: 10.1016/j.gene.2008.12.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 10/07/2008] [Accepted: 12/09/2008] [Indexed: 11/22/2022]
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