1
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Antine SP, Johnson AG, Mooney SE, Leavitt A, Mayer ML, Yirmiya E, Amitai G, Sorek R, Kranzusch PJ. Structural basis of Gabija anti-phage defence and viral immune evasion. Nature 2024; 625:360-365. [PMID: 37992757 PMCID: PMC10781630 DOI: 10.1038/s41586-023-06855-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 05/01/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation1-5. Gabija is one of the most prevalent anti-phage defence systems, occurring in more than 15% of all sequenced bacterial and archaeal genomes1,6,7, but the molecular basis of how Gabija defends cells from viral infection remains poorly understood. Here we use X-ray crystallography and cryo-electron microscopy (cryo-EM) to define how Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA. Gabija protein A (GajA) is a DNA endonuclease that tetramerizes to form the core of the anti-phage defence complex. Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo. We show that a phage-encoded protein, Gabija anti-defence 1 (Gad1), directly binds to the Gabija GajAB complex and inactivates defence. A cryo-EM structure of the virally inhibited state shows that Gad1 forms an octameric web that encases the GajAB complex and inhibits DNA recognition and cleavage. Our results reveal the structural basis of assembly of the Gabija anti-phage defence complex and define a unique mechanism of viral immune evasion.
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Affiliation(s)
- Sadie P Antine
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alex G Johnson
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah E Mooney
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Azita Leavitt
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Megan L Mayer
- Harvard Center for Cryo-Electron Microscopy, Harvard Medical School, Boston, MA, USA
| | - Erez Yirmiya
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, USA.
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2
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Wang Z, Geraghty RJ. Viral Nucleases. Viruses 2023; 15:v15030740. [PMID: 36992449 PMCID: PMC10052875 DOI: 10.3390/v15030740] [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: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
Nucleases are ubiquitous hydrolytic enzymes that cleave phosphodiester bond of DNA (DNases), RNA (RNases), or protein-RNA/DNA (phosphodiesterases), within the strand (endonucleases) or from the end (exonucleases) [...]
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3
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Lee J, Jo I, Ahn J, Hong S, Jeong S, Kwon A, Ha NC. Crystal structure of the nuclease and capping domain of SbcD from Staphylococcus aureus. J Microbiol 2021; 59:584-589. [PMID: 33877576 DOI: 10.1007/s12275-021-1012-0] [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: 01/08/2021] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 10/21/2022]
Abstract
The SbcCD complex is an essential component of the DNA double-strand break (DSB) repair system in bacteria. The bacterial SbcCD complex recognizes and cleaves the DNA ends in DSBs by ATP-dependent endo- and exonuclease activities as an early step of the DNA repair process. SbcD consists of nuclease, capping, and helix-loop-helix domains. Here, we present the crystal structure of a SbcD fragment from Staphylococcus aureus, which contained nuclease and capping domains, at a resolution of 2.9 Å. This structure shows a dimeric assembly similar to that of the corresponding domains of SbcD from Escherichia coli. The S. aureus SbcD fragment exhibited endonuclease activities on supercoiled DNA and exonuclease activity on linear and nicked DNA. This study contributes to the understanding of the molecular basis for how bacteria can resist sterilizing treatment, causing DNA damage.
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Affiliation(s)
- Jinwook Lee
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Inseong Jo
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea
- Current address: KoBioLabs, Inc., Seoul, 08826, Republic of Korea
| | - Jinsook Ahn
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seokho Hong
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soyeon Jeong
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Aeran Kwon
- Department of Beauty Care, College of Medical Science, Daegu Haany University, Gyeongsan, 38610, Republic of Korea
| | - Nam-Chul Ha
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea.
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4
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Zabolotnaya E, Mela I, Henderson RM, Robinson NP. Turning the Mre11/Rad50 DNA repair complex on its head: lessons from SMC protein hinges, dynamic coiled-coil movements and DNA loop-extrusion? Biochem Soc Trans 2020; 48:2359-2376. [PMID: 33300987 PMCID: PMC7752040 DOI: 10.1042/bst20170168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
The bacterial SbcC/SbcD DNA repair proteins were identified over a quarter of a century ago. Following the subsequent identification of the homologous Mre11/Rad50 complex in the eukaryotes and archaea, it has become clear that this conserved chromosomal processing machinery is central to DNA repair pathways and the maintenance of genomic stability in all forms of life. A number of experimental studies have explored this intriguing genome surveillance machinery, yielding significant insights and providing conceptual advances towards our understanding of how this complex operates to mediate DNA repair. However, the inherent complexity and dynamic nature of this chromosome-manipulating machinery continue to obfuscate experimental interrogations, and details regarding the precise mechanisms that underpin the critical repair events remain unanswered. This review will summarize our current understanding of the dramatic structural changes that occur in Mre11/Rad50 complex to mediate chromosomal tethering and accomplish the associated DNA processing events. In addition, undetermined mechanistic aspects of the DNA enzymatic pathways driven by this vital yet enigmatic chromosomal surveillance and repair apparatus will be discussed. In particular, novel and putative models of DNA damage recognition will be considered and comparisons will be made between the modes of action of the Rad50 protein and other related ATPases of the overarching SMC superfamily.
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Affiliation(s)
| | - Ioanna Mela
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, U.K
| | | | - Nicholas P. Robinson
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, U.K
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5
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Swartjes T, Staals RH, van der Oost J. Editor's cut: DNA cleavage by CRISPR RNA-guided nucleases Cas9 and Cas12a. Biochem Soc Trans 2020; 48:207-219. [PMID: 31872209 PMCID: PMC7054755 DOI: 10.1042/bst20190563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 12/26/2022]
Abstract
Discovered as an adaptive immune system of prokaryotes, CRISPR-Cas provides many promising applications. DNA-cleaving Cas enzymes like Cas9 and Cas12a, are of great interest for genome editing. The specificity of these DNA nucleases is determined by RNA guides, providing great targeting adaptability. Besides this general method of programmable DNA cleavage, these nucleases have different biochemical characteristics, that can be exploited for different applications. Although Cas nucleases are highly promising, some room for improvement remains. New developments and discoveries like base editing, prime editing, and CRISPR-associated transposons might address some of these challenges.
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Affiliation(s)
- Thomas Swartjes
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - Raymond H.J. Staals
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
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6
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Abstract
A bacterial biofilm is strongly associated with chronic infections and is difficult to be eradicated, posing serious threats to public health. Development of effective therapeutic strategies to prevent and control hospital-acquired infections via eradication of bacteria shielded by biofilms is challenging. Herein, we developed deoxyribonuclease (DNase)-functionalized gold nanoclusters (AuNCs) (DNase-AuNCs), which are capable of killing Gram-positive and Gram-negative bacteria, especially dispersing the surrounding biofilms. The DNase can break down the extracellular polymeric substance matrix to expose the defenseless bacteria to photothermal therapy (PTT) and photodynamic therapy (PDT) by DNase-AuNCs under 808 nm laser irradiation. The combination of enzymolysis, PDT, and PTT can effectively remove biofilms with a dispersion rate of up to 80% and kill ∼90% of the shielded bacteria. DNase-AuNCs exhibit an outstanding therapeutic effect in treating bacterial biofilm-coated orthodontic devices (Invisalign aligners), suggesting their potential applications in medical devices.
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Affiliation(s)
- Yangzhouyun Xie
- Department of Biomedical Engineering , Southern University of Science and Technology , No. 1088 Xueyuan Rd , Nanshan District, Shenzhen , Guangdong 518055 , P. R. China
- Beijing Engineering Research Center for BioNanotechnology and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , No. 11 Zhongguancun Beiyitiao , Beijing 100190 , P. R. China
| | - Wenfu Zheng
- Beijing Engineering Research Center for BioNanotechnology and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , No. 11 Zhongguancun Beiyitiao , Beijing 100190 , P. R. China
| | - Xingyu Jiang
- Department of Biomedical Engineering , Southern University of Science and Technology , No. 1088 Xueyuan Rd , Nanshan District, Shenzhen , Guangdong 518055 , P. R. China
- Beijing Engineering Research Center for BioNanotechnology and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , No. 11 Zhongguancun Beiyitiao , Beijing 100190 , P. R. China
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7
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Reuven N, Adler J, Broennimann K, Myers N, Shaul Y. Recruitment of DNA Repair MRN Complex by Intrinsically Disordered Protein Domain Fused to Cas9 Improves Efficiency of CRISPR-Mediated Genome Editing. Biomolecules 2019; 9:E584. [PMID: 31597252 PMCID: PMC6843829 DOI: 10.3390/biom9100584] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/02/2019] [Accepted: 10/05/2019] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 is a powerful tool for genome editing in cells and organisms. Nevertheless, introducing directed templated changes by homology-directed repair (HDR) requires the cellular DNA repair machinery, such as the MRN complex (Mre11/Rad50/Nbs1). To improve the process, we tailored chimeric constructs of Cas9, in which SpCas9 was fused at its N- or C-terminus to a 126aa intrinsically disordered domain from HSV-1 alkaline nuclease (UL12) that recruits the MRN complex. The chimeric Cas9 constructs were two times more efficient in homology-directed editing of endogenous loci in tissue culture cells. This effect was dependent upon the MRN-recruiting activity of the domain and required lower amounts of the chimeric Cas9 in comparison with unmodified Cas9. The new constructs improved the yield of edited cells when making endogenous point mutations or inserting small tags encoded by oligonucleotide donor DNA (ssODN), and also with larger insertions encoded by plasmid DNA donor templates. Improved editing was achieved with both transfected plasmid-encoded Cas9 constructs as well as recombinant Cas9 protein transfected as ribonucleoprotein complexes. Our strategy was highly efficient in restoring a genetic defect in a cell line, exemplifying the possible implementation of our strategy in gene therapy. These constructs provide a simple approach to improve directed editing.
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Affiliation(s)
- Nina Reuven
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Julia Adler
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Karin Broennimann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Nadav Myers
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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8
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Schiltz CJ, Lee A, Partlow EA, Hosford CJ, Chappie JS. Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage. Nucleic Acids Res 2019; 47:9448-9463. [PMID: 31400118 PMCID: PMC6755086 DOI: 10.1093/nar/gkz703] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 01/07/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022] Open
Abstract
Overcoming lysogenization defect (OLD) proteins constitute a family of uncharacterized nucleases present in bacteria, archaea, and some viruses. These enzymes contain an N-terminal ATPase domain and a C-terminal Toprim domain common amongst replication, recombination, and repair proteins. The in vivo activities of OLD proteins remain poorly understood and no definitive structural information exists. Here we identify and define two classes of OLD proteins based on differences in gene neighborhood and amino acid sequence conservation and present the crystal structures of the catalytic C-terminal regions from the Burkholderia pseudomallei and Xanthamonas campestris p.v. campestris Class 2 OLD proteins at 2.24 Å and 1.86 Å resolution respectively. The structures reveal a two-domain architecture containing a Toprim domain with altered architecture and a unique helical domain. Conserved side chains contributed by both domains coordinate two bound magnesium ions in the active site of B. pseudomallei OLD in a geometry that supports a two-metal catalysis mechanism for cleavage. The spatial organization of these domains additionally suggests a novel mode of DNA binding that is distinct from other Toprim containing proteins. Together, these findings define the fundamental structural properties of the OLD family catalytic core and the underlying mechanism controlling nuclease activity.
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Affiliation(s)
- Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - April Lee
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Edward A Partlow
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
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9
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Abstract
G-quadruplexes are four-stranded guanine-rich structures that have been demonstrated to occur across the genome in humans and other organisms. They provide regulatory functions during transcription, translation and immunoglobulin gene rearrangement, but there is also a large amount of evidence that they can present a potent barrier to the DNA replication machinery. This mini-review will summarize recent advances in understanding the many strategies nature has evolved to overcome G-quadruplex-mediated replication blockage, including removal of the structure by helicases or nucleases, or circumventing the deleterious effects on the genome through homologous recombination, alternative end-joining or synthesis re-priming. Paradoxically, G-quadruplexes have also recently been demonstrated to provide a positive role in stimulating the initiation of DNA replication. These recent studies have not only illuminated the many roles and consequences of G-quadruplexes, but have also provided fundamental insights into the general mechanisms of DNA replication and its links with genetic and epigenetic stability.
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Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia.
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10
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Yan JN, Han JR, Jiang XY, Shang WH, Jin WG, Du YN, Wu HT. Involvement of DNA in Gel Formation of Scallop ( Patinopecten yessoensis) Male Gonad Hydrolysates and Corresponding Hybrid Gel with κ-Carrageenan. J Agric Food Chem 2019; 67:7935-7941. [PMID: 31264423 DOI: 10.1021/acs.jafc.8b06543] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 06/09/2023]
Abstract
Involvement of DNA in gelation and microstructural properties of scallop (Patinopecten yessoensis) male gonad hydrolysates (SMGHs) and corresponding hybrid gel with κ-carrageenan (SMGHs/κ-C) was studied using DNase pretreatment. Although DNase pretreatment significantly transformed SMGHs from weak gels to liquid, it made SMGHs have a superior synergistic effect on gel formation with κ-C by evidence of 2.7-fold G' and 1.1-fold melting temperature. However, the relaxation time (T21 and T23), functional groups, and flocculation behavior were comparable between SMGHs/κ-C and SMGHs/DNase/κ-C. Moreover, SMGHs/DNase/κ-C exhibited a denser network with more numerous patches and larger void spaces. These results suggest that DNA contributes to the gel formation of SMGHs whereas restricts more cationic peptides in SMGHs to bind sulfate groups in κ-C during gel formation.
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Affiliation(s)
- Jia-Nan Yan
- School of Food Science and Technology , Dalian Polytechnic University , Dalian , Liaoning 116034 , People's Republic of China
| | - Jia-Run Han
- School of Food Science and Technology , Dalian Polytechnic University , Dalian , Liaoning 116034 , People's Republic of China
| | - Xin-Yu Jiang
- School of Food Science and Technology , Dalian Polytechnic University , Dalian , Liaoning 116034 , People's Republic of China
| | - Wen-Hui Shang
- School of Food Science and Technology , Dalian Polytechnic University , Dalian , Liaoning 116034 , People's Republic of China
| | - Wen-Gang Jin
- School of Bioscience and Engineering , Shaanxi University of Technology , Hanzhong , Shaanxi 723000 , People's Republic of China
| | - Yi-Nan Du
- School of Food Science and Technology , Dalian Polytechnic University , Dalian , Liaoning 116034 , People's Republic of China
| | - Hai-Tao Wu
- School of Food Science and Technology , Dalian Polytechnic University , Dalian , Liaoning 116034 , People's Republic of China
- National Engineering Research Center of Seafood , Dalian , Liaoning 116034 , People's Republic of China
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11
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Abstract
Tissue decellularization allows isolation of tissue extracellular matrix components, enabling bioengineering of native tissue microenvironments with minimal antigenic components. Here we describe a method to harvest decellularized cartilage tissue from donor trachea using a series of chemical and enzymatic washes and incorporating the extracellular matrix in gelatin methacrylate hydrogels. This decellularized cartilage tissue is easily incorporated into a variety of hydrogels to create a cartilage tissue scaffold.
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Affiliation(s)
- Zachary Galliger
- Department of Pediatrics, Blood and Marrow Transplant Program, University of Minnesota, Mayo Mail Code 366, 420 Delaware Street SE, Minneapolis, MN, 55455, USA
| | - Angela Panoskaltsis-Mortari
- Department of Pediatrics, Blood and Marrow Transplant Program, University of Minnesota, Mayo Mail Code 366, 420 Delaware Street SE, Minneapolis, MN, 55455, USA.
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12
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Yan WX, Hunnewell P, Alfonse LE, Carte JM, Keston-Smith E, Sothiselvam S, Garrity AJ, Chong S, Makarova KS, Koonin EV, Cheng DR, Scott DA. Functionally diverse type V CRISPR-Cas systems. Science 2019; 363:88-91. [PMID: 30523077 DOI: 10.1126/science.aav7271] [Citation(s) in RCA: 260] [Impact Index Per Article: 52.0] [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: 10/14/2018] [Accepted: 11/20/2018] [Indexed: 01/05/2024]
Abstract
Type V CRISPR-Cas systems are distinguished by a single RNA-guided RuvC domain-containing effector, Cas12. Although effectors of subtypes V-A (Cas12a) and V-B (Cas12b) have been studied in detail, the distinct domain architectures and diverged RuvC sequences of uncharacterized Cas12 proteins suggest unexplored functional diversity. Here, we identify and characterize Cas12c, -g, -h, and -i. Cas12c, -h, and -i demonstrate RNA-guided double-stranded DNA (dsDNA) interference activity. Cas12i exhibits markedly different efficiencies of CRISPR RNA spacer complementary and noncomplementary strand cleavage resulting in predominant dsDNA nicking. Cas12g is an RNA-guided ribonuclease (RNase) with collateral RNase and single-strand DNase activities. Our study reveals the functional diversity emerging along different routes of type V CRISPR-Cas evolution and expands the CRISPR toolbox.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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13
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Abstract
Despite their relative simplicity, iron-sulfur clusters have been omnipresent as cofactors in myriad cellular processes such as oxidative phosphorylation and other respiratory pathways. Recent research advances confirm the presence of different clusters in enzymes involved in nucleic acid metabolism. Iron-sulfur clusters can therefore be considered hallmarks of cellular metabolism. Helicases, nucleases, glycosylases, DNA polymerases and transcription factors, among others, incorporate various types of clusters that serve differing roles. In this chapter, we review our current understanding of the identity and functions of iron-sulfur clusters in DNA and RNA metabolizing enzymes, highlighting their importance as regulators of cellular function.
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Affiliation(s)
- Yara Khodour
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine.
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14
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Saathoff JH, Käshammer L, Lammens K, Byrne RT, Hopfner KP. The bacterial Mre11-Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions. Nucleic Acids Res 2018; 46:11303-11314. [PMID: 30277537 PMCID: PMC6265447 DOI: 10.1093/nar/gky878] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 06/06/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022] Open
Abstract
The Mre11-Rad50 complex is a DNA double-strand break sensor that cleaves blocked DNA ends and hairpins by an ATP-dependent endo/exonuclease activity for subsequent repair. For that, Mre11-Rad50 complexes, including the Escherichia coli homolog SbcCD, can endonucleolytically cleave one or both strands near a protein block and process free DNA ends via a 3'-5' exonuclease, but a unified basis for these distinct activities is lacking. Here we analyzed DNA binding, ATPase and nuclease reactions on different DNA substrates. SbcCD clips terminal bases of both strands of the DNA end in the presence of ATPγS. It introduces a DNA double-strand break around 20-25 bp from a blocked end after multiple rounds of ATP hydrolysis in a reaction that correlates with local DNA meltability. Interestingly, we find that nuclease reactions on opposing strands are chemically distinct, leaving a 5' phosphate on one strand, but a 3' phosphate on the other strand. Collectively, our results identify an unexpected chemical variability of the nuclease, indicating that the complex is oriented at a free DNA end and facing a block with opposite polarity. This suggests a unified model for ATP-dependent endo- and exonuclease reactions at internal DNA near a block and at free DNA ends.
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Affiliation(s)
- Jan-Hinnerk Saathoff
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Lisa Käshammer
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Katja Lammens
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Robert Thomas Byrne
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Karl-Peter Hopfner
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Center for Integrated Protein Science, Munich, Germany
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15
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Sotnichenko AS, Nakokhov RZ, Gubareva EA, Kuevda EV, Gumenyuk IS. Morphological Evaluation of the Tissue Reaction to Subcutaneous Implantation of Decellularized Matrices. Bull Exp Biol Med 2018; 166:287-292. [PMID: 30488196 DOI: 10.1007/s10517-018-4334-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 12/19/2017] [Indexed: 11/25/2022]
Abstract
Based on the data of morphological analysis, we performed histological evaluation of rat tissue reaction to subcutaneous implantation of decellularized matrices of intrathoracic organs and tissues. Cell composition of the inflammatory infiltrate was analyzed, and the dynamics of macrophage and T and B lymphocyte content was assessed on days 7 and 14 of the experiment. It was found that the reaction to implantation depended not only on the quality of decellularization and efficiency of removal of antigen molecules, but also on the original histological structure and quality of preimplantation processing of the transplant.
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Affiliation(s)
| | - R Z Nakokhov
- Kuban State Medical University, Krasnodar, Russia
| | - E A Gubareva
- Kuban State Medical University, Krasnodar, Russia
| | - E V Kuevda
- Kuban State Medical University, Krasnodar, Russia
| | - I S Gumenyuk
- Kuban State Medical University, Krasnodar, Russia
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16
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Nakahata DH, de Paiva REF, Lustri WR, Ribeiro CM, Pavan FR, da Silva GG, Ruiz ALTG, de Carvalho JE, Corbi PP. Sulfonamide-containing copper(II) metallonucleases: Correlations with in vitro antimycobacterial and antiproliferative activities. J Inorg Biochem 2018; 187:85-96. [PMID: 30081333 DOI: 10.1016/j.jinorgbio.2018.07.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 03/16/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/25/2022]
Abstract
The bis-(1,10-phenanthroline)copper(I) complex, [Cu(I)(phen)2]+, was the first copper-based artificial nuclease reported in the literature. The biological and ligand-like properties of sulfonamides make them good candidates for fine-tuning the reactivity of the [Cu(phen)2] motif with biomolecules. In this context, we developed three novel copper(II) complexes containing the sulfonamides sulfameter (smtrH) and sulfadimethoxine (sdmxH) and (N^N)-bidentate ligands (2,2'-biyridine or 1,10-phenantroline). The compounds were characterized by chemical and spectroscopic techniques and single-crystal X-ray crystallography. When targeting plasmid DNA, the phen-containing compounds [Cu(smtr-)2(phen)] (1) and [Cu(sdmx-)2(phen)] (2) demonstrated nuclease activity even in the absence of reducing agents. Addition of ascorbic acid resulted in a complete cleavage of DNA by 1 and 2 at concentrations higher than 10 μM. Experiments designed to evaluate the copper intermediates involved in the nuclease effect after reaction with ascorbic acid identified at least the [Cu(I)(N^N)2]+, [Cu(I)(sulfa)(N^N)]+ and [Cu(I)(sulfa)2]+ species. The compounds interact with DNA via groove binding and intercalation as verified by fluorescence spectroscopy, circular dichroism (CD) and molecular docking. The magnitude and preferred mode of binding are dependent on the nature of both N^N ligand and the sulfonamide. The potent nuclease activity of compounds 1 and 2 are well correlated with their antiproliferative and anti-M. tuberculosis profiles. The results presented here demonstrated the potential for further development of copper(II)-sulfonamide-(N^N) complexes as multipurpose metallodrugs.
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Affiliation(s)
- Douglas H Nakahata
- Institute of Chemistry, University of Campinas, UNICAMP, 13083-970 Campinas, SP, Brazil
| | - Raphael E F de Paiva
- Institute of Chemistry, University of Campinas, UNICAMP, 13083-970 Campinas, SP, Brazil
| | - Wilton R Lustri
- Biological and Health Sciences Department, University of Araraquara, UNIARA, 14801-320 Araraquara, SP, Brazil
| | - Camila M Ribeiro
- School of Pharmaceutical Sciences, São Paulo State University, UNESP, 14800-901 Araraquara, SP, Brazil
| | - Fernando R Pavan
- School of Pharmaceutical Sciences, São Paulo State University, UNESP, 14800-901 Araraquara, SP, Brazil
| | - Gisele G da Silva
- Faculty of Pharmaceutical Sciences, University of Campinas, UNICAMP, 13081-970 Campinas, SP, Brazil; Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), University of Campinas - UNICAMP, 13148-218 Paulínia, SP, Brazil; Department of Physiological Sciences, Piracicaba Dental School, University of Campinas, UNICAMP, 13414-903, Piracicaba, SP, Brazil
| | - Ana L T G Ruiz
- Faculty of Pharmaceutical Sciences, University of Campinas, UNICAMP, 13081-970 Campinas, SP, Brazil; Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), University of Campinas - UNICAMP, 13148-218 Paulínia, SP, Brazil
| | - João E de Carvalho
- Faculty of Pharmaceutical Sciences, University of Campinas, UNICAMP, 13081-970 Campinas, SP, Brazil
| | - Pedro P Corbi
- Institute of Chemistry, University of Campinas, UNICAMP, 13083-970 Campinas, SP, Brazil.
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17
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Sun B, Qian X, Zhu F. Molecular characterization of shrimp harbinger transposase derived 1 (HARBI1)-like and its role in white spot syndrome virus and Vibrio alginolyticus infection. Fish Shellfish Immunol 2018; 78:222-232. [PMID: 29680489 DOI: 10.1016/j.fsi.2018.04.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/09/2018] [Accepted: 04/18/2018] [Indexed: 06/08/2023]
Abstract
The role of the nuclease, HARBI1-like protein (mjHARBI1-like) in the innate immunity of Marsupenaeus japonicus was explored in this study. The 1361 bp cDNA sequence of mjHARBI1-like was cloned from M. japonicus using RACE. RT-qPCR analysis results showed that the gills and hepatopancreas of M. japonicus were the main tissues where mjHARBI1-like is expressed. In addition, it was also found that white spot syndrome virus (WSSV) or Vibrio alginolyticus challenge could stimulate mjHARBI1-like expression. After mjHARBI1-likewas inhibited, expression of immune genes such as toll, p53, myosin, and proPO were significantly downregulated (P < 0.01). However, in shrimp hemocytes, hemocyanin and tumor necrosis factor-α (TNF-α) were up-regulated significantly (P < 0.01). This study demonstrated that mjHARBI1-like plays a key role in the progression of WSSV and V. alginolyticus infection. Specifically, the cumulative mortality of WSSV-infected and V. alginolyticus-infected shrimp was significantly advanced by double-strand RNA interference (dsRNAi) of mjHARBI1-like. Apoptosis studies indicated that mjHARBI1-dsRNA treatment caused a reduction in hemocyte apoptosis in bacterial and viral groups. In addition, phagocytosis experiments illustrated that mjHARBI1-dsRNA treatment led to a lower phagocytosis rate in hemocytes of V. alginolyticus-challenged shrimp. It was also found that knockdown of mjHARBI1-like inhibited shrimp phenoloxidase (PO) activity, superoxide dismutase (SOD) activity, and total hemocyte count (THC) after WSSV or V. alginolyticus infection. These data indicate a regulative role of mjHARBI1-likein the immunity of shrimp in response to pathogen infection. Resultantly, it was concluded that mjHARBI1-like might have a positive effect on the anti-WSSV immune response of shrimp by regulating apoptosis, THC, PO activity, and SOD activity. Additionally, mjHARBI1-like might promote anti-V. alginolyticus infection by participating in regulating phagocytosis, apoptosis, SOD activity, PO activity, and THC.
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Affiliation(s)
- Baozhen Sun
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Xiyi Qian
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Fei Zhu
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China.
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18
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Bogdanove AJ, Bohm A, Miller JC, Morgan RD, Stoddard BL. Engineering altered protein-DNA recognition specificity. Nucleic Acids Res 2018; 46:4845-4871. [PMID: 29718463 PMCID: PMC6007267 DOI: 10.1093/nar/gky289] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 02/07/2023] Open
Abstract
Protein engineering is used to generate novel protein folds and assemblages, to impart new properties and functions onto existing proteins, and to enhance our understanding of principles that govern protein structure. While such approaches can be employed to reprogram protein-protein interactions, modifying protein-DNA interactions is more difficult. This may be related to the structural features of protein-DNA interfaces, which display more charged groups, directional hydrogen bonds, ordered solvent molecules and counterions than comparable protein interfaces. Nevertheless, progress has been made in the redesign of protein-DNA specificity, much of it driven by the development of engineered enzymes for genome modification. Here, we summarize the creation of novel DNA specificities for zinc finger proteins, meganucleases, TAL effectors, recombinases and restriction endonucleases. The ease of re-engineering each system is related both to the modularity of the protein and the extent to which the proteins have evolved to be capable of readily modifying their recognition specificities in response to natural selection. The development of engineered DNA binding proteins that display an ideal combination of activity, specificity, deliverability, and outcomes is not a fully solved problem, however each of the current platforms offers unique advantages, offset by behaviors and properties requiring further study and development.
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Affiliation(s)
- Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Bohm
- Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Jeffrey C Miller
- Sangamo Therapeutics Inc. 501 Canal Blvd., Richmond, CA 94804, USA
| | - Richard D Morgan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98019, USA
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19
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Miersch C, Stange K, Röntgen M. Effects of trypsinization and of a combined trypsin, collagenase, and DNase digestion on liberation and in vitro function of satellite cells isolated from juvenile porcine muscles. In Vitro Cell Dev Biol Anim 2018; 54:406-412. [PMID: 29785535 PMCID: PMC5997727 DOI: 10.1007/s11626-018-0263-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/02/2018] [Indexed: 12/27/2022]
Abstract
Muscle stem cells, termed satellite cells (SC), and SC-derived myogenic progenitor cells (MPC) are involved in postnatal muscle growth, regeneration, and muscle adaptability. They can be released from their natural environment by mechanical disruption and tissue digestion. The literature contains several isolation protocols for porcine SC/MPC including various digestion procedures, but comparative studies are missing. In this report, classic trypsinization and a more complex trypsin, collagenase, and DNase (TCD) digestion were performed with skeletal muscle tissue from 4- to 5-d-old piglets. The two digestion procedures were compared regarding cell yield, viability, myogenic purity, and in vitro cell function. The TCD digestion tended to result in higher cell yields than digestion with solely trypsin (statistical trend p = 0.096), whereas cell size and viability did not differ. Isolated myogenic cells from both digestion procedures showed comparable proliferation rates, expressed the myogenic marker Desmin, and initiated myogenic differentiation in vitro at similar levels. Thus, TCD digestion tended to liberate slightly more cells without changes in the tested in vitro properties of the isolated cells. Both procedures are adequate for the isolation of SC/MPC from juvenile porcine muscles but the developmental state of the animal should always be considered.
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Affiliation(s)
- Claudia Miersch
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Muscle Biology and Growth, Growth and Development Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Katja Stange
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Muscle Biology and Growth, Growth and Development Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Monika Röntgen
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Muscle Biology and Growth, Growth and Development Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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20
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Guan RB, Li HC, Fan YJ, Hu SR, Christiaens O, Smagghe G, Miao XX. A nuclease specific to lepidopteran insects suppresses RNAi. J Biol Chem 2018; 293:6011-6021. [PMID: 29500196 PMCID: PMC5912458 DOI: 10.1074/jbc.ra117.001553] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [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: 12/27/2017] [Revised: 02/26/2018] [Indexed: 12/12/2022] Open
Abstract
More than 70% of all agricultural pests are insects in the order Lepidoptera, which, unlike other related insect orders, are not very sensitive to RNAi, limiting genetic studies of this insect group. However, the reason for this distinct lepidopteran characteristic is unknown. Previously, using transcriptome analysis of the Asian corn borer Ostrinia furnacalis, we identified a gene, termed up56, that is up-regulated in response to dsRNA. Here we report that this Lepidoptera-specific gene encodes a nuclease that contributes to RNAi insensitivity in this insect order. Its identity was experimentally validated, and sequence analysis indicated that up56 encodes a previously uncharacterized protein with homologous sequences in seven other lepidopteran species. Its computationally predicted three-dimensional structure revealed a high structural similarity to human exonuclease I. Exposure to dsRNA in O. furnacalis strongly up-regulated this gene's expression, and the protein could digest single-stranded RNA (ssRNA), dsRNA, and dsDNA both in vitro and in vivo Of note, we found that this up-regulation of up56 expression is faster than that of the gene encoding the key RNAi-associated nuclease Dicer. up56 knockdown in O. furnacalis significantly enhanced RNAi efficiency. Moreover, up56 overexpression in Drosophila melanogaster suppressed RNAi efficiency. Finally, up56 knockdown significantly increased the amount and diversity of small RNAs. Therefore, we renamed this protein RNAi efficiency-related nuclease (REase). In conclusion, we propose that REase may explain why lepidopterans are refractory to RNAi and that it represents a target for further research of RNAi efficiency in this insect order.
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Affiliation(s)
- Ruo-Bing Guan
- From the Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hai-Chao Li
- From the Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu-Jie Fan
- From the Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shao-Ru Hu
- From the Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- the University of the Chinese Academy of Sciences, Beijing 100049, China, and
| | - Olivier Christiaens
- the Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Guy Smagghe
- the Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Xue-Xia Miao
- From the Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China,
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21
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Kougentakis CM, Grasso EM, Robinson AC, Caro JA, Schlessman JL, Majumdar A, García-Moreno E B. Anomalous Properties of Lys Residues Buried in the Hydrophobic Interior of a Protein Revealed with 15N-Detect NMR Spectroscopy. J Phys Chem Lett 2018; 9:383-387. [PMID: 29266956 DOI: 10.1021/acs.jpclett.7b02668] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 06/07/2023]
Abstract
Ionizable residues buried in hydrophobic environments in proteins are essential for many fundamental biochemical processes. These residues titrate with anomalous pKa values that are challenging to reproduce with structure-based calculations owing to the conformational reorganization coupled to their ionization. Detailed characterization of this conformational reorganization is of interest; unfortunately, the properties of buried Lys residues are difficult to study experimentally. Here we demonstrate the utility of 15N NMR spectroscopy to gain insight into the protonation state, state of hydration and conformational dynamics of the Nζ amino group of buried Lys residues. The experiments were applied to five variants of staphylococcal nuclease, with internal Lys residues that titrate with pKa values ranging from 6.2 to 8.1. Direct detection of buried Lys residues with these NMR spectroscopy methods will enable correlation between thermodynamic and structural data as well as unprecedented examination of how conformational transitions coupled to their ionization affect their pKa values.
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Affiliation(s)
| | | | | | | | - Jamie L Schlessman
- Chemistry Department, United States Naval Academy , 572M Holloway Rd MS 9B, Annapolis, Maryland 21402, United States
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22
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Marti E, Ferrary-Américo M, Barardi CRM. Detection of Potential Infectious Enteric Viruses in Fresh Produce by (RT)-qPCR Preceded by Nuclease Treatment. Food Environ Virol 2017; 9:444-452. [PMID: 28452009 DOI: 10.1007/s12560-017-9300-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
Foodborne illnesses associated with contaminated fresh produce are a common public health problem and there is an upward trend of outbreaks caused by enteric viruses, especially human noroviruses (HNoVs) and hepatitis A virus (HAV). This study aimed to assess the use of DNase and RNase coupled to qPCR and RT-qPCR, respectively, to detect intact particles of human adenoviruses (HAdVs), HNoV GI and GII and HAV in fresh produce. Different concentrations of DNase and RNase were tested to optimize the degradation of free DNA and RNA from inactivated HAdV and murine norovirus (MNV), respectively. Results indicated that 10 µg/ml of RNase was able to degrade more than 4 log10 (99.99%) of free RNA, and 1 U of DNase degraded the range of 0.84-2.5 log10 of free DNA depending on the fresh produce analysed. The treatment with nucleases coupled to (RT)-qPCR was applied to detect potential infectious virus in organic lettuce, green onions and strawberries collected in different seasons. As a result, no intact particles of HNoV GI and GII were detected in the 36 samples analysed, HAdV was found in one sample and HAV was present in 33.3% of the samples, without any reasonable distribution pattern among seasons. In conclusion, RT-qPCR preceded by RNase treatment of eluted samples from fresh produce is a good alternative to detect undamaged RNA viruses and therefore, potential infectious viruses. Moreover, this study provides data about the prevalence of enteric viruses in organic fresh produce from Brazil.
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Affiliation(s)
- Elisabet Marti
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, CEP: 88040-970, Brazil.
| | - Monique Ferrary-Américo
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, CEP: 88040-970, Brazil
| | - Célia Regina Monte Barardi
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, CEP: 88040-970, Brazil
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23
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Niyonzima N, Lambert AR, Werther R, De Silva Feelixge H, Roychoudhury P, Greninger AL, Stone D, Stoddard BL, Jerome KR. Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses. Protein Eng Des Sel 2017; 30:503-522. [PMID: 28873986 PMCID: PMC5914421 DOI: 10.1093/protein/gzx037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [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: 03/15/2017] [Revised: 06/19/2017] [Accepted: 07/06/2017] [Indexed: 11/14/2022] Open
Abstract
The combination of yeast surface display and flow cytometric analyses and selections is being used with increasing frequency to alter specificity of macromolecular recognition, including both protein-protein and protein-nucleic acid interactions. Here we describe the use of yeast surface display and cleavage-dependent flow cytometric assays to increase the specificity of an engineered meganuclease. The re-engineered meganuclease displays a significantly tightened specificity profile, while binding its cognate target site with a slightly lower, but still sub-nanomolar affinity. When incorporated into otherwise identical megaTAL protein scaffolds, these two nucleases display significantly different activity and toxicity profiles in cellulo. The structural basis for reprogrammed DNA cleavage specificity was further examined via high-resolution X-ray crystal structures of both enzymes. This analysis illustrated the altered protein-DNA contacts produced by mutagenesis and selection, that resulted both in altered readout of those based and a necessary reduction in DNA binding affinity that were necessary to improve specificity across the target site. The results of this study provide an illustrative example of the potential (and the challenges) associated with the use of surface display and flow cytometry for the retargeting and optimization of enzymes that act on nucleic acid substrates in a sequence-specific manner.
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Affiliation(s)
- Nixon Niyonzima
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Abigail R. Lambert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Rachel Werther
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Harshana De Silva Feelixge
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Alexander L. Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
- Virology Division, Department of Laboratory Medicine, University of Washington, 1616 Eastlake Ave. E, Seattle WA 98102, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Barry L. Stoddard
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
- Virology Division, Department of Laboratory Medicine, University of Washington, 1616 Eastlake Ave. E, Seattle WA 98102, USA
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24
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Abstract
Adaptive immune systems in bacteria and archaea rely on small CRISPR-derived RNAs (crRNAs) to guide specialized nucleases to foreign nucleic acids. The activation of these nucleases is controlled by a series of molecular checkpoints that ensure precise cleavage of nucleic acid targets, while minimizing toxic off-target cleavage events. In this review, we highlight recent advances in understanding regulatory mechanisms responsible for controlling the activation of these nucleases and identify emerging regulatory themes conserved across diverse CRISPR systems.
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Affiliation(s)
- Ryan N Jackson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, United States.
| | - Paul Bg van Erp
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, United States.
| | | | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, United States.
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25
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Gubendran A, Kesavan MP, Ayyanaar S, Mitu L, Athappan P, Rajesh J. Non-enolisable Knoevenagel condensate appended Schiff bases-metal (II) complexes: Spectral characteristics, DNA-binding and nuclease activities. Spectrochim Acta A Mol Biomol Spectrosc 2017; 181:39-46. [PMID: 28319797 DOI: 10.1016/j.saa.2017.03.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/14/2017] [Accepted: 03/14/2017] [Indexed: 06/06/2023]
Abstract
New Schiff base complexes [Cu(L1)Cl] (1), [Ni(L1)Cl] (2), [Zn(L1)Cl] (3), and [Fe(L2)H2OCl] (4) {L1=(4E)-3-(2-hydroxybenzylidene)-4-(2-hydroxyphenylimino)pentan-2-one, L2=2,2'-(1E,1'E)-(3-(2-hydroxybenzylidene)-pentane-2,4-diylidene)bis(azan-1-yl-1 idene)diphenol} have been synthesized and characterized by elemental analysis, UV-Vis, IR, FAB-mass, EPR, spectral studies and electrochemical studies, the ligands L1 &L2 were characterized by 1H and 13C NMR spectra. Complex 1 show a visible spectral d-d band near 600nm and display cyclic voltammetric quasireversible response for the Cu(II)/Cu(I) couple vs Ag/AgCl in DMSO. The EPR spectrum of 1 show g‖>g⊥ suggesting a square planar geometry around copper with dx2-y2 as the ground state. The mass spectral results have confirmed the proposed structure for complexes 1-4. DNA binding properties of these complexes 1-4 have been investigated by absorption titrations, cyclic voltammetric studies and circular dichroism studies. On titration with DNA, the complexes 1-4 show hypochromism at the MLCT band (13-31%) with a red shift of 1-8nm in the electronic spectrum and positive shift of voltammetric E1/2 in the CV studies are in favour of intercalative binding. CD spectra of 1 showed an increase in molar ellipticity (θ278) of the positive band with a minor red shift indicating the transition of B-form of DNA to A like form. DNA cleavage studies of complexes 1 and 4 with pUC18 DNA were studied by gel electrophoresis and complex 4 cleaves supercoiled pUC18 DNA in an oxidative manner in the presence of H2O2 and on photo irradiation at 312nm.
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Affiliation(s)
- Ammavasi Gubendran
- Department of Inorganic Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai 625 021, India; Department of Chemistry, Saraswathi Narayanan College, Madurai 625 022, India
| | | | - Srinivasan Ayyanaar
- Chemistry Research Centre, Mohamed Sathak Engineering College, Kilakarai 623 806, Tamilnadu, India
| | - Liviu Mitu
- Department of Physics and Chemistry, University of Pitesti, Pitesti 110040, Romania
| | - Periyakaruppan Athappan
- Department of Inorganic Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai 625 021, India
| | - Jegathalaprathaban Rajesh
- Department of Inorganic Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai 625 021, India; Chemistry Research Centre, Mohamed Sathak Engineering College, Kilakarai 623 806, Tamilnadu, India.
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26
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Brown RV, Wang T, Chappeta VR, Wu G, Onel B, Chawla R, Quijada H, Camp SM, Chiang ET, Lassiter QR, Lee C, Phanse S, Turnidge MA, Zhao P, Garcia JGN, Gokhale V, Yang D, Hurley LH. The Consequences of Overlapping G-Quadruplexes and i-Motifs in the Platelet-Derived Growth Factor Receptor β Core Promoter Nuclease Hypersensitive Element Can Explain the Unexpected Effects of Mutations and Provide Opportunities for Selective Targeting of Both Structures by Small Molecules To Downregulate Gene Expression. J Am Chem Soc 2017; 139:7456-7475. [PMID: 28471683 PMCID: PMC5977998 DOI: 10.1021/jacs.6b10028] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [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] [Indexed: 12/14/2022]
Abstract
The platelet-derived growth factor receptor β (PDGFR-β) signaling pathway is a validated and important target for the treatment of certain malignant and nonmalignant pathologies. We previously identified a G-quadruplex-forming nuclease hypersensitive element (NHE) in the human PDGFR-β promoter that putatively forms four overlapping G-quadruplexes. Therefore, we further investigated the structures and biological roles of the G-quadruplexes and i-motifs in the PDGFR-β NHE with the ultimate goal of demonstrating an alternate and effective strategy for molecularly targeting the PDGFR-β pathway. Significantly, we show that the primary G-quadruplex receptor for repression of PDGFR-β is the 3'-end G-quadruplex, which has a GGA sequence at the 3'-end. Mutation studies using luciferase reporter plasmids highlight a novel set of G-quadruplex point mutations, some of which seem to provide conflicting results on effects on gene expression, prompting further investigation into the effect of these mutations on the i-motif-forming strand. Herein we characterize the formation of an equilibrium between at least two different i-motifs from the cytosine-rich (C-rich) sequence of the PDGFR-β NHE. The apparently conflicting mutation results can be rationalized if we take into account the single base point mutation made in a critical cytosine run in the PDGFR-β NHE that dramatically affects the equilibrium of i-motifs formed from this sequence. We identified a group of ellipticines that targets the G-quadruplexes in the PDGFR-β promoter, and from this series of compounds, we selected the ellipticine analog GSA1129, which selectively targets the 3'-end G-quadruplex, to shift the dynamic equilibrium in the full-length sequence to favor this structure. We also identified a benzothiophene-2-carboxamide (NSC309874) as a PDGFR-β i-motif-interactive compound. In vitro, GSA1129 and NSC309874 downregulate PDGFR-β promoter activity and transcript in the neuroblastoma cell line SK-N-SH at subcytotoxic cell concentrations. GSA1129 also inhibits PDGFR-β-driven cell proliferation and migration. With an established preclinical murine model of acute lung injury, we demonstrate that GSA1129 attenuates endotoxin-mediated acute lung inflammation. Our studies underscore the importance of considering the effects of point mutations on structure formation from the G- and C-rich sequences and provide further evidence for the involvement of both strands and associated structures in the control of gene expression.
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Affiliation(s)
- Robert V. Brown
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Ting Wang
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | | | - Guanhui Wu
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Buket Onel
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Reena Chawla
- BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721, United States
| | - Hector Quijada
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Sara M. Camp
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Eddie T. Chiang
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Quinea R. Lassiter
- College of Agriculture & Life Sciences, University of Arizona, 1117 East Lowell Street, Tucson, Arizona 85721, United States
| | - Carmen Lee
- College of Agriculture & Life Sciences, University of Arizona, 1117 East Lowell Street, Tucson, Arizona 85721, United States
- College of Science, University of Arizona, 1040 East Fourth Street, Tucson, Arizona 85721, United States
| | - Shivani Phanse
- College of Science, University of Arizona, 1040 East Fourth Street, Tucson, Arizona 85721, United States
| | - Megan A. Turnidge
- College of Science, University of Arizona, 1040 East Fourth Street, Tucson, Arizona 85721, United States
| | - Ping Zhao
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, No. 280 Waihuandong Road, Education Mega Centre, Guanzhou 510006, Peoples Republic of China
| | - Joe G. N. Garcia
- College of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Vijay Gokhale
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
- BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721, United States
| | - Danzhou Yang
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
- BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Laurence H. Hurley
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
- BIO5 Institute, 1657 East Helen Street, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
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27
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Marze NA, Jeliazkov JR, Roy Burman SS, Boyken SE, DiMaio F, Gray JJ. Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35. Proteins 2017; 85:479-486. [PMID: 27667482 PMCID: PMC5710743 DOI: 10.1002/prot.25168] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 07/27/2016] [Revised: 09/01/2016] [Accepted: 09/26/2016] [Indexed: 12/27/2022]
Abstract
The 28th-35th rounds of the Critical Assessment of PRotein Interactions (CAPRI) served as a practical benchmark for our RosettaDock protein-protein docking protocols, highlighting strengths and weaknesses of the approach. We achieved acceptable or better quality models in three out of 11 targets. For the two α-repeat protein-green fluorescent protein (αrep-GFP) complexes, we used a novel ellipsoidal partial-global docking method (Ellipsoidal Dock) to generate models with 2.2 Å/1.5 Å interface RMSD, capturing 49%/42% of the native contacts, for the 7-/5-repeat αrep complexes. For the DNase-immunity protein complex, we used a new predictor of hydrogen-bonding networks, HBNet with Bridging Waters, to place individual water models at the complex interface; models were generated with 1.8 Å interface RMSD and 12% native water contacts recovered. The targets for which RosettaDock failed to create an acceptable model were typically difficult in general, as six had no acceptable models submitted by any CAPRI predictor. The UCH-L5-RPN13 and UCH-L5-INO80G de-ubiquitinating enzyme-inhibitor complexes comprised inhibitors undergoing significant structural changes upon binding, with the partners being highly interwoven in the docked complexes. Our failure to predict the nucleosome-enzyme complex in Target 95 was largely due to tight constraints we placed on our model based on sparse biochemical data suggesting two specific cross-interface interactions, preventing the correct structure from being sampled. While RosettaDock's three successes show that it is a state-of-the-art docking method, the difficulties with highly flexible and multi-domain complexes highlight the need for better flexible docking and domain-assembly methods. Proteins 2017; 85:479-486. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nicholas A. Marze
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Jeliazko R. Jeliazkov
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Shourya S. Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Scott E. Boyken
- Department of Biochemistry, University of Washington, Seattle, Washington
- Institute for Protein Design, University of Washington, Seattle, Washington
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington
- Institute for Protein Design, University of Washington, Seattle, Washington
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
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28
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Abstract
The identification of conventional dendritic cells (cDCs) and macrophages (mϕ) in the intestinal mucosa has been hampered by the difficulties associated with isolating cells from the intestine and by the fact that overlapping markers have made it complicated to discriminate them accurately from each other and from other intestinal myeloid cells. Here we detail the protocols we have developed to isolate live leukocytes from steady state mouse small and large intestines and describe reliable strategies which can be used to identify bona fide cDCs, monocytes and macrophages in such preparations.
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Affiliation(s)
- Charlotte L Scott
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Veterinary, Medical and Life Sciences, University of Glasgow, Scotland, UK
- Inflammation Research Centre (IRC), Laboratory of Immunoregulation, VIB Ghent University, Ghent (Zwijnaarde), 9052, Belgium
| | - Calum C Bain
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Veterinary, Medical and Life Sciences, University of Glasgow, Scotland, UK
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, Scotland, UK
| | - Allan McI Mowat
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Veterinary, Medical and Life Sciences, University of Glasgow, Scotland, UK.
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29
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Rideout MC, Liet B, Gasparutto D, Berthet N. A high-throughput screen for detection of compound-dependent phosphodiester bond cleavage at abasic sites. Anal Biochem 2016; 513:93-97. [PMID: 27594348 DOI: 10.1016/j.ab.2016.08.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 02/16/2016] [Revised: 07/28/2016] [Accepted: 08/30/2016] [Indexed: 11/20/2022]
Abstract
We have employed a DNA molecular beacon with a real abasic site, namely a 2-deoxyribose, in a fluorescent high-throughput assay to identify artificial nucleases that cleave at abasic sites. We screened a 1280 compound chemical library and identified a compound that functions as an artificial nuclease. We validated a key structure-activity relationship necessary for abasic site cleavage using available analogs of the identified artificial nuclease. We also addressed the activity of the identified compound with dose titrations in the absence and presence of a source of non-specific DNA. Finally, we characterized the phosphodiester backbone cleavage at the abasic site using denaturing gel electrophoresis. This study provides a useful template for researchers seeking to rapidly identify new artificial nucleases.
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Affiliation(s)
- Marc C Rideout
- Département de Chimie Moléculaire (DCM), Laboratoire Ingénierie et Interactions BioMoléculaires (I2BM), UMR-5250, ICMG FR-2607, CNRS, Université Grenoble Alpes (UGA), 570 Rue de la Chimie, BP-53, 38041 Grenoble Cedex 9, France.
| | - Benjamin Liet
- Département de Chimie Moléculaire (DCM), Laboratoire Ingénierie et Interactions BioMoléculaires (I2BM), UMR-5250, ICMG FR-2607, CNRS, Université Grenoble Alpes (UGA), 570 Rue de la Chimie, BP-53, 38041 Grenoble Cedex 9, France
| | - Didier Gasparutto
- Institut des Nanosciences & Cryogénie (INAC), SPrAM - UMR 5819 CEA/CNRS/Université Grenoble Alpes, Commissariat à l'Energie Atomique, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Nathalie Berthet
- Département de Chimie Moléculaire (DCM), Laboratoire Ingénierie et Interactions BioMoléculaires (I2BM), UMR-5250, ICMG FR-2607, CNRS, Université Grenoble Alpes (UGA), 570 Rue de la Chimie, BP-53, 38041 Grenoble Cedex 9, France.
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30
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Noges LE, White J, Cambier JC, Kappler JW, Marrack P. Contamination of DNase Preparations Confounds Analysis of the Role of DNA in Alum-Adjuvanted Vaccines. J Immunol 2016; 197:1221-30. [PMID: 27357147 PMCID: PMC4974487 DOI: 10.4049/jimmunol.1501565] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 06/02/2016] [Indexed: 11/19/2022]
Abstract
Aluminum salt (alum) adjuvants have been used for many years as adjuvants for human vaccines because they are safe and effective. Despite its widespread use, the means by which alum acts as an adjuvant remains poorly understood. Recently, it was shown that injected alum is rapidly coated with host chromatin within mice. Experiments suggested that the host DNA in the coating chromatin contributed to alum's adjuvant activity. Some of the experiments used commercially purchased DNase and showed that coinjection of these DNase preparations with alum and Ag reduced the host's immune response to the vaccine. In this study, we report that some commercial DNase preparations are contaminated with proteases. These proteases are responsible for most of the ability of DNase preparations to inhibit alum's adjuvant activity. Nevertheless, DNase somewhat reduces responses to some Ags with alum. The effect of DNase is independent of its ability to cleave DNA, suggesting that alum improves CD4 responses to Ag via a pathway other than host DNA sensing.
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Affiliation(s)
- Laura E Noges
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206; Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045; and
| | - Janice White
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - John C Cambier
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206; Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045; and
| | - John W Kappler
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206; Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045; and Howard Hughes Medical Institute, National Jewish Health, Denver, CO 80206
| | - Philippa Marrack
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206; Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045; and Howard Hughes Medical Institute, National Jewish Health, Denver, CO 80206
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31
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Bednarski C, Tomczak K, vom Hövel B, Weber WM, Cathomen T. Targeted Integration of a Super-Exon into the CFTR Locus Leads to Functional Correction of a Cystic Fibrosis Cell Line Model. PLoS One 2016; 11:e0161072. [PMID: 27526025 PMCID: PMC4985144 DOI: 10.1371/journal.pone.0161072] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 06/13/2016] [Accepted: 07/29/2016] [Indexed: 01/04/2023] Open
Abstract
In vitro disease models have enabled insights into the pathophysiology of human disease as well as the functional evaluation of new therapies, such as novel genome engineering strategies. In the context of cystic fibrosis (CF), various cellular disease models have been established in recent years, including organoids based on induced pluripotent stem cell technology that allowed for functional readouts of CFTR activity. Yet, many of these in vitro CF models require complex and expensive culturing protocols that are difficult to implement and may not be amenable for high throughput screens. Here, we show that a simple cellular CF disease model based on the bronchial epithelial ΔF508 cell line CFBE41o- can be used to validate functional CFTR correction. We used an engineered nuclease to target the integration of a super-exon, encompassing the sequences of CFTR exons 11 to 27, into exon 11 and re-activated endogenous CFTR expression by treating CFBE41o- cells with a demethylating agent. We demonstrate that the integration of this super-exon resulted in expression of a corrected mRNA from the endogenous CFTR promoter and used short-circuit current measurements in Ussing chambers to corroborate restored ion transport of the repaired CFTR channels. In conclusion, this study proves that the targeted integration of a large super-exon in CFTR exon 11 leads to functional correction of CFTR, suggesting that this strategy can be used to functionally correct all CFTR mutations located downstream of the 5' end of exon 11.
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Affiliation(s)
- Christien Bednarski
- Institute for Cell and Gene Therapy, Medical Center–University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center–University of Freiburg, Freiburg, Germany
| | - Katja Tomczak
- Institute of Animal Physiology, Westphalian Wilhelms-University, Muenster, Germany
| | - Beate vom Hövel
- Institute for Cell and Gene Therapy, Medical Center–University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center–University of Freiburg, Freiburg, Germany
| | - Wolf-Michael Weber
- Institute of Animal Physiology, Westphalian Wilhelms-University, Muenster, Germany
| | - Toni Cathomen
- Institute for Cell and Gene Therapy, Medical Center–University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center–University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
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32
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Zhang H, Zhao G, Guo Y, Menghwar H, Chen Y, Chen H, Guo A. Mycoplasma bovis MBOV_RS02825 Encodes a Secretory Nuclease Associated with Cytotoxicity. Int J Mol Sci 2016; 17:ijms17050628. [PMID: 27136546 PMCID: PMC4881454 DOI: 10.3390/ijms17050628] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 01/08/2023] Open
Abstract
This study aimed to determine the activity of one Mycoplasma bovis nuclease encoded by MBOV_RS02825 and its association with cytotoxicity. The bioinformatics analysis predicted that it encodes a Ca2+-dependent nuclease based on existence of enzymatic sites in a TNASE_3 domain derived from a Staphylococcus aureus thermonuclease (SNc). We cloned and purified the recombinant MbovNase (rMbovNase), and demonstrated its nuclease activity by digesting bovine macrophage linear DNA and RNA, and closed circular plasmid DNA in the presence of 10 mM Ca2+ at 22–65 °C. In addition, this MbovNase was localized in membrane and rMbovNase able to degrade DNA matrix of neutrophil extracellular traps (NETs). When incubated with macrophages, rMbovNase bound to and invaded the cells localizing to both the cytoplasm and nuclei. These cells experienced apoptosis and the viability was significantly reduced. The apoptosis was confirmed by activated expression of phosphorylated NF-κB p65 and Bax, and inhibition of Iκβα and Bcl-2. In contrast, rMbovNaseΔ181–342 without TNASE_3 domain exhibited deficiency in all the biological functions. Furthermore, rMbovNase was also demonstrated to be secreted. In conclusion, it is a first report that MbovNase is an active nuclease, both secretory and membrane protein with ability to degrade NETs and induce apoptosis.
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Affiliation(s)
- Hui Zhang
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Gang Zhao
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yusi Guo
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Harish Menghwar
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan 430070, China.
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Huanchun Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan 430070, China.
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan 430070, China.
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China.
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33
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Garrido-Baserba M, Asvapathanagul P, McCarthy GW, Gocke TE, Olson BH, Park HD, Al-Omari A, Murthy S, Bott CB, Wett B, Smeraldi JD, Shaw AR, Rosso D. Linking biofilm growth to fouling and aeration performance of fine-pore diffuser in activated sludge. Water Res 2016; 90:317-328. [PMID: 26760484 DOI: 10.1016/j.watres.2015.12.011] [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] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 11/18/2015] [Accepted: 12/09/2015] [Indexed: 06/05/2023]
Abstract
Aeration is commonly identified as the largest contributor to process energy needs in the treatment of wastewater and therefore garners significant focus in reducing energy use. Fine-pore diffusers are the most common aeration system in municipal wastewater treatment. These diffusers are subject to fouling and scaling, resulting in loss in transfer efficiency as biofilms form and change material properties producing larger bubbles, hindering mass transfer and contributing to increased plant energy costs. This research establishes a direct correlation and apparent mechanistic link between biofilm DNA concentration and reduced aeration efficiency caused by biofilm fouling. Although the connection between biofilm growth and fouling has been implicit in discussions of diffuser fouling for many years, this research provides measured quantitative connection between the extent of biofouling and reduced diffuser efficiency. This was clearly established by studying systematically the deterioration of aeration diffusers efficiency during a 1.5 year period, concurrently with the microbiological study of the biofilm fouling in order to understand the major factors contributing to diffuser fouling. The six different diffuser technologies analyzed in this paper included four different materials which were ethylene-propylene-diene monomer (EPDM), polyurethane, silicone and ceramic. While all diffusers foul eventually, some novel materials exhibited fouling resistance. The material type played a major role in determining the biofilm characteristics (i.e., growth rate, composition, and microbial density) which directly affected the rate and intensity at what the diffusers were fouled, whereas diffuser geometry exerted little influence. Overall, a high correlation between the increase in biofilm DNA and the decrease in αF was evident (CV < 14.0 ± 2.0%). By linking bacterial growth with aeration efficiency, the research was able to show quantitatively the causal connection between bacterial fouling and energy wastage during aeration.
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Affiliation(s)
- Manel Garrido-Baserba
- Department of Civil & Environmental Engineering, University of California, Irvine, CA 92697-2175, USA.
| | - Pitiporn Asvapathanagul
- Department of Civil & Environmental Engineering, University of California, Irvine, CA 92697-2175, USA; Department of Civil Engineering and Construction Engineering Management, California State University, Long Beach, CA 90840, USA
| | - Graham W McCarthy
- Department of Civil & Environmental Engineering, University of California, Irvine, CA 92697-2175, USA
| | - Thomas E Gocke
- Department of Civil & Environmental Engineering, University of California, Irvine, CA 92697-2175, USA
| | - Betty H Olson
- Department of Civil & Environmental Engineering, University of California, Irvine, CA 92697-2175, USA; Water-Energy Nexus Center, University of California, Irvine, CA 92697-2175, USA
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-713, South Korea
| | - Ahmed Al-Omari
- DC Water, 5000 Overlook Ave SW, Washington, DC 20032, USA
| | - Sudhir Murthy
- DC Water, 5000 Overlook Ave SW, Washington, DC 20032, USA
| | - Charles B Bott
- Hampton Roads Sanitation District, Virginia Beach, VA 23471-0911, USA
| | - Bernhard Wett
- ARAconsult, Unterbergerstraße 1, A-6020 Innsbruck, Austria
| | - Joshua D Smeraldi
- United States Environmental Protection Agency, 1200 Pennsylvania Ave NW, Washington, DC 20460, USA
| | - Andrew R Shaw
- Black & Veatch, 8400 Ward Pkwy, Kansas City, MO 64114, USA
| | - Diego Rosso
- Department of Civil & Environmental Engineering, University of California, Irvine, CA 92697-2175, USA; Water-Energy Nexus Center, University of California, Irvine, CA 92697-2175, USA.
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Ma L, Zhu F, Li Z, Zhang J, Li X, Dong J, Wang T. TALEN-Based Mutagenesis of Lipoxygenase LOX3 Enhances the Storage Tolerance of Rice (Oryza sativa) Seeds. PLoS One 2015; 10:e0143877. [PMID: 26641666 PMCID: PMC4671593 DOI: 10.1371/journal.pone.0143877] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [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: 08/25/2015] [Accepted: 11/10/2015] [Indexed: 12/23/2022] Open
Abstract
The deterioration of rice grain reduces the quality of rice, resulting in serious economic losses for farmers. Lipoxygenases (LOXs) catalyze the dioxygenation of polyunsaturated fatty acids with at least one cis,cis-1,4-pentadiene to form hydroperoxide, which is a major factor influencing seed longevity and viability. Recently, genome editing, an essential tool employed in reverse genetics, has been used experimentally to investigate basic plant biology or to modify crop plants for the improvement of important agricultural traits. In this study, we performed targeted mutagenesis in rice using transcription activator-like effector nucleases (TALENs) to improve seed storability. A modified ligation-independent cloning method (LIC) was employed to allow for the quick and efficient directional insertion of TALEN monomer modules into destination vectors used in plants. We demonstrated the feasibility and flexibility of the technology by developing a set of modular vectors for genome editing. After construction and validation, the TALEN pairs were used to create stable transgenic rice lines via Agrobacterium-mediated transformation. One heterozygous mutant (4%) was recovered from 25 transgenic NPTII-resistant lines, and the mutation was transmitted to the next generation. Further molecular and protein level experiments verified LOX3 deficiency and demonstrated the improvement of seed storability. Our work provides a flexible genome editing tool for improving important agronomic traits, as well as direct evidence that Lox3 has only a limited impact on seed longevity.
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Affiliation(s)
- Lei Ma
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Fugui Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhenwei Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jianfu Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xin Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiangli Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Tao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- * E-mail:
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Lee G, Cho S, Hoang PM, Kim D, Lee Y, Kil EJ, Byun SJ, Lee TK, Kim DH, Kim S, Lee S. Therapeutic Strategy for the Prevention of Pseudorabies Virus Infection in C57BL/6 Mice by 3D8 scFv with Intrinsic Nuclease Activity. Mol Cells 2015; 38:773-80. [PMID: 26255831 PMCID: PMC4588720 DOI: 10.14348/molcells.2015.0073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/09/2015] [Accepted: 06/22/2015] [Indexed: 11/27/2022] Open
Abstract
3D8 single chain variable fragment (scFv) is a recombinant monoclonal antibody with nuclease activity that was originally isolated from autoimmune-prone MRL mice. In a previous study, we analyzed the nuclease activity of 3D8 scFv and determined that a HeLa cell line expressing 3D8 scFv conferred resistance to herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV). In this study, we demonstrate that 3D8 scFv could be delivered to target tissues and cells where it exerted a therapeutic effect against PRV. PRV was inoculated via intramuscular injection, and 3D8 scFv was injected intraperitoneally. The observed therapeutic effect of 3D8 scFv against PRV was also supported by results from quantitative reverse transcription polymerase chain reaction, southern hybridization, and immunohistochemical assays. Intraperitoneal injection of 5 and 10 μg 3D8 scFv resulted in no detectable toxicity. The survival rate in C57BL/6 mice was 9% after intramuscular injection of 10 LD50 PRV. In contrast, the 3D8 scFv-injected C57BL/6 mice showed survival rates of 57% (5 μg) and 47% (10 μg). The results indicate that 3D8 scFv could be utilized as an effective antiviral agent in several animal models.
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Affiliation(s)
- Gunsup Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 440-746,
Korea
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 440-706,
Korea
| | - SeungChan Cho
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 440-746,
Korea
| | - Phuong Mai Hoang
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 440-746,
Korea
| | - Dongjun Kim
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 440-746,
Korea
| | - Yongjun Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 440-746,
Korea
| | - Eui-Joon Kil
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 440-746,
Korea
| | - Sung-June Byun
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706,
Korea
| | - Taek-Kyun Lee
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje 656-834,
Korea
| | - Dae-Hyun Kim
- Fruit Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 440-706,
Korea
| | - Sunghan Kim
- Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921,
Korea
| | - Sukchan Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 440-746,
Korea
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Dansithong W, Paul S, Scoles DR, Pulst SM, Huynh DP. Generation of SNCA Cell Models Using Zinc Finger Nuclease (ZFN) Technology for Efficient High-Throughput Drug Screening. PLoS One 2015; 10:e0136930. [PMID: 26317803 PMCID: PMC4552753 DOI: 10.1371/journal.pone.0136930] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 09/09/2014] [Accepted: 08/10/2015] [Indexed: 12/17/2022] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder caused by loss of dopaminergic neurons of the substantia nigra. The hallmark of PD is the appearance of neuronal protein aggregations known as Lewy bodies and Lewy neurites, of which α-synuclein forms a major component. Familial PD is rare and is associated with missense mutations of the SNCA gene or increases in gene copy number resulting in SNCA overexpression. This suggests that lowering SNCA expression could be therapeutic for PD. Supporting this hypothesis, SNCA reduction was neuroprotective in cell line and rodent PD models. We developed novel cell lines expressing SNCA fused to the reporter genes luciferase (luc) or GFP with the objective to enable high-throughput compound screening (HTS) for small molecules that can lower SNCA expression. Because SNCA expression is likely regulated by far-upstream elements (including the NACP-REP1 located at 8852 bp upstream of the transcription site), we employed zinc finger nuclease (ZFN) genome editing to insert reporter genes in-frame downstream of the SNCA gene in order to retain native SNCA expression control. This ensured full retention of known and unknown up- and downstream genetic elements controlling SNCA expression. Treatment of cells with the histone deacetylase inhibitor valproic acid (VPA) resulted in significantly increased SNCA-luc and SNCA-GFP expression supporting the use of our cell lines for identifying small molecules altering complex modes of expression control. Cells expressing SNCA-luc treated with a luciferase inhibitor or SNCA siRNA resulted in Z'-scores ≥ 0.75, suggesting the suitability of these cell lines for use in HTS. This study presents a novel use of genome editing for the creation of cell lines expressing α-synuclein fusion constructs entirely under native expression control. These cell lines are well suited for HTS for compounds that lower SNCA expression directly or by acting at long-range sites to the SNCA promoter and 5'-UTR.
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Affiliation(s)
- Warunee Dansithong
- Department of Neurology, University of Utah, 175 North Medical Center Drive East, 5th Floor, Salt Lake City, Utah, 84132, United States of America
| | - Sharan Paul
- Department of Neurology, University of Utah, 175 North Medical Center Drive East, 5th Floor, Salt Lake City, Utah, 84132, United States of America
| | - Daniel R. Scoles
- Department of Neurology, University of Utah, 175 North Medical Center Drive East, 5th Floor, Salt Lake City, Utah, 84132, United States of America
| | - Stefan M. Pulst
- Department of Neurology, University of Utah, 175 North Medical Center Drive East, 5th Floor, Salt Lake City, Utah, 84132, United States of America
| | - Duong P. Huynh
- Department of Neurology, University of Utah, 175 North Medical Center Drive East, 5th Floor, Salt Lake City, Utah, 84132, United States of America
- * E-mail:
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Ghosh K, Tyagi N, Kumar H, Rathi S. DNA interaction, SOD, peroxidase and nuclease activity studies of iron complex having ligand with carboxamido nitrogen donors. Spectrochim Acta A Mol Biomol Spectrosc 2015; 146:292-296. [PMID: 25819318 DOI: 10.1016/j.saa.2015.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 12/09/2014] [Accepted: 03/01/2015] [Indexed: 06/04/2023]
Abstract
Complex (Et3HN)[Fe(III)(bpb)Cl2], 1 {where H2bpb: N,N'-(1,2-phenylene)bis(pyridine-2-carboxamide)} was synthesized and characterized by reported procedure (Yang et al., 1991). Complex 1 was found to be effective in superoxide scavenging activity and an IC50 value of 4.1 μM was obtained in xanthine-xanthine oxidase nitro blue tetrazolium assay. Peroxidase-like activity of this complex was determined by the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS). DNA interaction studies of complex 1 showed binding of DNA through external or groove binding. Complex 1 exhibited chemical nuclease activity in the presence of hydrogen peroxide and cleaved supercoiled pBR322 DNA to its linear and nicked circular form at physiological pH. Mechanistic studies indicated possible role of hydroxyl radical (·OH) species in DNA cleavage activity via hydroperoxo intermediate: [Fe(III)OOH(-)](2+)→[Fe(IV)O](2+)+(·)OH.
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Affiliation(s)
- Kaushik Ghosh
- Department of Chemistry, Indian Institute of Technology, Roorkee, Roorkee 247667, Uttarakhand, India.
| | - Nidhi Tyagi
- Department of Chemistry, Indian Institute of Technology, Roorkee, Roorkee 247667, Uttarakhand, India
| | - Hemant Kumar
- Department of Chemistry, Indian Institute of Technology, Roorkee, Roorkee 247667, Uttarakhand, India
| | - Sweety Rathi
- Department of Chemistry, Indian Institute of Technology, Roorkee, Roorkee 247667, Uttarakhand, India
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Mock U, Machowicz R, Hauber I, Horn S, Abramowski P, Berdien B, Hauber J, Fehse B. mRNA transfection of a novel TAL effector nuclease (TALEN) facilitates efficient knockout of HIV co-receptor CCR5. Nucleic Acids Res 2015; 43:5560-71. [PMID: 25964300 PMCID: PMC4477672 DOI: 10.1093/nar/gkv469] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [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: 01/10/2015] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 12/12/2022] Open
Abstract
Homozygosity for a natural deletion variant of the HIV-coreceptor molecule CCR5, CCR5Δ32, confers resistance toward HIV infection. Allogeneic stem cell transplantation from a CCR5Δ32-homozygous donor has resulted in the first cure from HIV ('Berlin patient'). Based thereon, genetic disruption of CCR5 using designer nucleases was proposed as a promising HIV gene-therapy approach. Here we introduce a novel TAL-effector nuclease, CCR5-Uco-TALEN that can be efficiently delivered into T cells by mRNA electroporation, a gentle and truly transient gene-transfer technique. CCR5-Uco-TALEN mediated high-rate CCR5 knockout (>90% in PM1 and >50% in primary T cells) combined with low off-target activity, as assessed by flow cytometry, next-generation sequencing and a newly devised, very convenient gene-editing frequency digital-PCR (GEF-dPCR). GEF-dPCR facilitates simultaneous detection of wild-type and gene-edited alleles with remarkable sensitivity and accuracy as shown for the CCR5 on-target and CCR2 off-target loci. CCR5-edited cells were protected from infection with HIV-derived lentiviral vectors, but also with the wild-type CCR5-tropic HIV-1BaL strain. Long-term exposure to HIV-1BaL resulted in almost complete suppression of viral replication and selection of CCR5-gene edited T cells. In conclusion, we have developed a novel TALEN for the targeted, high-efficiency knockout of CCR5 and a useful dPCR-based gene-editing detection method.
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Affiliation(s)
- Ulrike Mock
- Research Dept. Cell and Gene Therapy, Dept. of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Rafał Machowicz
- Research Dept. Cell and Gene Therapy, Dept. of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany Department of Hematology, Oncology and Internal Medicine, Medical University of Warsaw, 02-097, Poland
| | - Ilona Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, 20251, Germany
| | - Stefan Horn
- Research Dept. Cell and Gene Therapy, Dept. of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Pierre Abramowski
- Research Dept. Cell and Gene Therapy, Dept. of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Belinda Berdien
- Research Dept. Cell and Gene Therapy, Dept. of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Joachim Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, 20251, Germany German Center for Infection Research (DZIF), partner site Hamburg, Hamburg, Germany
| | - Boris Fehse
- Research Dept. Cell and Gene Therapy, Dept. of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
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Li C, Rowland MJ, Shao Y, Cao T, Chen C, Jia H, Zhou X, Yang Z, Scherman OA, Liu D. Responsive Double Network Hydrogels of Interpenetrating DNA and CB[8] Host-Guest Supramolecular Systems. Adv Mater 2015; 27:3298-3304. [PMID: 25899855 DOI: 10.1002/adma.201501102] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 03/30/2015] [Indexed: 06/04/2023]
Abstract
A supramolecular double network hydrogel is presented by physical interpenetration of DNA and cucurbit[8]uril networks. In addition to exhibiting an increase in strength and thermal stability, the double network hydrogel possesses excellent properties such as stretchability, ductility, shear-thinning, and thixotropy. Moreover, it is enzymatically responsive to both nuclease and cellulase, as well as small molecules, showing great potential as a new soft material scaffold.
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Affiliation(s)
- Chuang Li
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Matthew J Rowland
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Yu Shao
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Tianyang Cao
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Chun Chen
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Haoyang Jia
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Xu Zhou
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
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Vikneswaran R, Syafiq MS, Eltayeb NE, Kamaruddin MN, Ramesh S, Yahya R. A new thio-Schiff base fluorophore with copper ion sensing, DNA binding and nuclease activity. Spectrochim Acta A Mol Biomol Spectrosc 2015; 150:175-180. [PMID: 26046495 DOI: 10.1016/j.saa.2015.05.087] [Citation(s) in RCA: 7] [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] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/13/2015] [Accepted: 05/20/2015] [Indexed: 06/04/2023]
Abstract
Copper ion recognition and DNA interaction of a newly synthesized fluorescent Schiff base (HPyETSC) were investigated using UV-vis and fluorescent spectroscopy. Examination using these two techniques revealed that the detection of copper by HPyETSC is highly sensitive and selective, with a detection limit of 0.39 μm and the mode of interaction between HPyETSC and DNA is electrostatic, with a binding constant of 8.97×10(4) M(-1). Furthermore, gel electrophoresis studies showed that HPyETSC exhibited nuclease activity through oxidative pathway.
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Affiliation(s)
- R Vikneswaran
- Centre for Ionics University of Malaya, Department of Physics, Faculty of Science, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Muhamad Syamir Syafiq
- Centre for Ionics University of Malaya, Department of Physics, Faculty of Science, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
| | - Naser Eltaher Eltayeb
- Department of Chemistry, Sciences & Arts College - Rabigh, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Mohd Naqiuddin Kamaruddin
- Centre for Ionics University of Malaya, Department of Physics, Faculty of Science, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
| | - S Ramesh
- Centre for Ionics University of Malaya, Department of Physics, Faculty of Science, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - R Yahya
- Department of Chemistry, Faculty of Science, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
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41
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Yang H, Liang W, He N, Deng Y, Li Z. Chemiluminescent labels released from long spacer arm-functionalized magnetic particles: a novel strategy for ultrasensitive and highly selective detection of pathogen infections. ACS Appl Mater Interfaces 2015; 7:774-781. [PMID: 25553360 DOI: 10.1021/am507203s] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 06/04/2023]
Abstract
Previously, the unique advantages provided by chemiluminescence (CL) and magnetic particles (MPs) have resulted in the development of many useful nucleic acid detection methods. CL is highly sensitive, but when applied to MPs, its intensity is limited by the inner filter-like effect arising from excess dark MPs. Herein, we describe a modified strategy whereby CL labels are released from MPs to eliminate this negative effect. This approach relies on (1) the magnetic capture of target molecules on long spacer arm-functionalized magnetic particles (LSA-MPs), (2) the conjugation of streptavidin-alkaline phosphatase (SA-AP) to biotinylated amplicons of target pathogens, (3) the release of CL labels (specifically, AP tags), and (4) the detection of the released labels. CL labels were released from LSA-MPs through LSA ultrasonication or DNA enzymolysis, which proved to be the superior method. In contrast to conventional MPs, LSA-MPs exhibited significantly improved CL detection, because of the introduction of LSA, which was made of water-soluble carboxymethylated β-1,3-glucan. Detection of hepatitis B virus with this technique revealed a low detection limit of 50 fM, high selectivity, and excellent reproducibility. Thus, this approach may hold great potential for early stage clinical diagnosis of infectious diseases.
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Affiliation(s)
- Haowen Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
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42
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Gonzalez-Vasconcellos I, Alonso-Rodríguez S, López-Baltar I, Fernández JL. Telomere Chromatin Condensation Assay (TCCA): a novel approach to study structural telomere integrity. Mutat Res 2015; 771:51-55. [PMID: 25771980 DOI: 10.1016/j.mrfmmm.2014.12.004] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/02/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
Telomeres, the DNA-protein complexes located at the end of linear eukaryotic chromosomes are essential for genome stability. Improper higher-order chromatin organization at the chromosome ends can give rise to telomeric recombination and genomic instability. We report the development of an assay to quantify differences in the condensation of telomeric chromatin, thereby offering new opportunities to study telomere biology and stability. We have combined a DNA nuclease digestion with a quantitative PCR (qPCR) assay of telomeric DNA, which we term the Telomere Chromatin Condensation Assay (TCCA). By quantifying the relative quantities of telomeric DNA that are progressively digested with the exonuclease Bal 31 the method can discriminate between different levels of telomeric chromatin condensation. The structural chromatin packaging at telomeres shielded against exonuclease digestion delivered an estimate, which we term Chromatin Protection Factor (CPF) that ranged from 1.7 to 2.3 fold greater than that present in unpacked DNA. The CPF was significantly decreased when cell cultures were incubated with the DNA hypomethylating agent 5-azacytidine, demonstrating the ability of the TCCA assay to discriminate between packaging levels of telomeric DNA.
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Affiliation(s)
- Iria Gonzalez-Vasconcellos
- INIBIC-Complejo Hospitalario Universitario A Coruña, Unidad de Genética, As Xubias, 84, 15006 A Coruña, Spain
| | - Silvia Alonso-Rodríguez
- INIBIC-Complejo Hospitalario Universitario A Coruña, Unidad de Genética, As Xubias, 84, 15006 A Coruña, Spain
| | - Isidoro López-Baltar
- Laboratorio de Genética Molecular y Radiobiología, Centro Oncológico de Galicia, 15009 A Coruña, Spain
| | - José Luis Fernández
- INIBIC-Complejo Hospitalario Universitario A Coruña, Unidad de Genética, As Xubias, 84, 15006 A Coruña, Spain; Laboratorio de Genética Molecular y Radiobiología, Centro Oncológico de Galicia, 15009 A Coruña, Spain.
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Thomas HR, Percival SM, Yoder BK, Parant JM. High-throughput genome editing and phenotyping facilitated by high resolution melting curve analysis. PLoS One 2014; 9:e114632. [PMID: 25503746 PMCID: PMC4263700 DOI: 10.1371/journal.pone.0114632] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [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: 09/30/2014] [Accepted: 11/12/2014] [Indexed: 02/01/2023] Open
Abstract
With the goal to generate and characterize the phenotypes of null alleles in all genes within an organism and the recent advances in custom nucleases, genome editing limitations have moved from mutation generation to mutation detection. We previously demonstrated that High Resolution Melting (HRM) analysis is a rapid and efficient means of genotyping known zebrafish mutants. Here we establish optimized conditions for HRM based detection of novel mutant alleles. Using these conditions, we demonstrate that HRM is highly efficient at mutation detection across multiple genome editing platforms (ZFNs, TALENs, and CRISPRs); we observed nuclease generated HRM positive targeting in 1 of 6 (16%) open pool derived ZFNs, 14 of 23 (60%) TALENs, and 58 of 77 (75%) CRISPR nucleases. Successful targeting, based on HRM of G0 embryos correlates well with successful germline transmission (46 of 47 nucleases); yet, surprisingly mutations in the somatic tail DNA weakly correlate with mutations in the germline F1 progeny DNA. This suggests that analysis of G0 tail DNA is a good indicator of the efficiency of the nuclease, but not necessarily a good indicator of germline alleles that will be present in the F1s. However, we demonstrate that small amplicon HRM curve profiles of F1 progeny DNA can be used to differentiate between specific mutant alleles, facilitating rare allele identification and isolation; and that HRM is a powerful technique for screening possible off-target mutations that may be generated by the nucleases. Our data suggest that micro-homology based alternative NHEJ repair is primarily utilized in the generation of CRISPR mutant alleles and allows us to predict likelihood of generating a null allele. Lastly, we demonstrate that HRM can be used to quickly distinguish genotype-phenotype correlations within F1 embryos derived from G0 intercrosses. Together these data indicate that custom nucleases, in conjunction with the ease and speed of HRM, will facilitate future high-throughput mutation generation and analysis needed to establish mutants in all genes of an organism.
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Affiliation(s)
- Holly R. Thomas
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Stefanie M. Percival
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Bradley K. Yoder
- Department of Cellular, Developmental, and Integrated Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - John M. Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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Ravichandran J, Gurumoorthy P, Imran Musthafa MA, Kalilur Rahiman A. Antioxidant, DNA binding and nuclease activities of heteroleptic copper(II) complexes derived from 2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols and diimines. Spectrochim Acta A Mol Biomol Spectrosc 2014; 133:785-793. [PMID: 24998685 DOI: 10.1016/j.saa.2014.06.045] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 05/27/2014] [Accepted: 06/03/2014] [Indexed: 06/03/2023]
Abstract
A series of heteroleptic copper(II) complexes of the type [CuL(1-4)(diimine)](ClO4)2 (1-8) [L(1-4)=2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols, and diimine=2,2'-bipyridyl (bpy) or 1,10-phenanthroline (phen)], have been synthesized and characterized by spectroscopic methods. The IR spectra of complexes indicate the presence of uncoordinated perchlorate anions and the electronic spectra revealed the square pyramidal geometry with N4O coordination environment around copper(II) nuclei. Electrochemical studies of the mononuclear complexes evidenced one-electron irreversible reduction wave in the cathodic region. The EPR spectra of complexes with g|| (2.206-2.214) and A|| (154-172×10(-)(4)cm(-)(1)) values support the square-based CuN3O coordination chromophore and the presence of unpaired electron localized in [Formula: see text] ground state. Antioxidant studies against DPPH revealed effective radical scavenging properties of the synthesized complexes. Binding studies suggest that the heteroleptic copper(II) complexes interact with calf thymus DNA (CT-DNA) through minor-groove and electrostatic interaction, and all the complexes display pronounced nuclease activity against supercoiled pBR322 DNA.
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Affiliation(s)
- J Ravichandran
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), Chennai 600 014, India; Research and Development Department, Amrutanjan Healthcare Limited, Mylapore, Chennai 600 004, India
| | - P Gurumoorthy
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), Chennai 600 014, India
| | - M A Imran Musthafa
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), Chennai 600 014, India
| | - A Kalilur Rahiman
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), Chennai 600 014, India.
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Burkova EE, Dmitrenok PS, Sedykh SE, Buneva VN, Soboleva SE, Nevinsky GA. Extremely stable soluble high molecular mass multi-protein complex with DNase activity in human placental tissue. PLoS One 2014; 9:e111234. [PMID: 25426722 PMCID: PMC4245193 DOI: 10.1371/journal.pone.0111234] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [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: 08/18/2014] [Accepted: 09/26/2014] [Indexed: 01/06/2023] Open
Abstract
Human placenta is an organ which protects, feeds, and regulates the grooving of the embryo. Therefore, identification and characterization of placental components including proteins and their multi-protein complexes is an important step to understanding the placenta function. We have obtained and analyzed for the first time an extremely stable multi-protein complex (SPC, ∼1000 kDa) from the soluble fraction of three human placentas. By gel filtration on Sepharose-4B, the SPC was well separated from other proteins of the placenta extract. Light scattering measurements and gel filtration showed that the SPC is stable in the presence of NaCl, MgCl2, acetonitrile, guanidinium chloride, and Triton in high concentrations, but dissociates efficiently in the presence of 8 M urea, 50 mM EDTA, and 0.5 M NaCl. Such a stable complex is unlikely to be a casual associate of different proteins. According to SDS-PAGE and MALDI mass spectrometry data, this complex contains many major glycosylated proteins with low and moderate molecular masses (MMs) 4–14 kDa and several moderately abundant (79.3, 68.5, 52.8, and 27.2 kDa) as well as minor proteins with higher MMs. The SPC treatment with dithiothreitol led to a disappearance of some protein bands and revealed proteins with lower MMs. The SPCs from three placentas efficiently hydrolyzed plasmid supercoiled DNA with comparable rates and possess at least two DNA-binding sites with different affinities for a 12-mer oligonucleotide. Progress in study of placental protein complexes can promote understanding of their biological functions.
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Affiliation(s)
- Evgeniya E. Burkova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Pavel S. Dmitrenok
- Pacific Institute of Bioorganic Chemistry, Far East Division, Russian Academy of Sciences, Vladivostok, Russia
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Valentina N. Buneva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Svetlana E. Soboleva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Georgy A. Nevinsky
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail:
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46
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Seong CS, Varela-Ramirez A, Tang X, Anchondo B, Magallanes D, Aguilera RJ. Cloning and characterization of a novel Drosophila stress induced DNase. PLoS One 2014; 9:e103564. [PMID: 25083901 PMCID: PMC4118900 DOI: 10.1371/journal.pone.0103564] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 07/04/2014] [Indexed: 01/04/2023] Open
Abstract
Drosophila melanogaster flies mount an impressive immune response to a variety of pathogens with an efficient system comprised of both humoral and cellular responses. The fat body is the main producer of the anti-microbial peptides (AMPs) with anti-pathogen activity. During bacterial infection, an array of secreted peptidases, proteases and other enzymes are involved in the dissolution of debris generated by pathogen clearance. Although pathogen destruction should result in the release a large amount of nucleic acids, the mechanisms for its removal are still not known. In this report, we present the characterization of a nuclease gene that is induced not only by bacterial infection but also by oxidative stress. Expression of the identified protein has revealed that it encodes a potent nuclease that has been named Stress Induced DNase (SID). SID belongs to a family of evolutionarily conserved cation-dependent nucleases that degrade both single and double-stranded nucleic acids. Down-regulation of sid expression via RNA interference leads to significant reduction of fly viability after bacterial infection and oxidative stress. Our results indicate that SID protects flies from the toxic effects of excess DNA/RNA released by pathogen destruction and from oxidative damage.
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Affiliation(s)
- Chang-Soo Seong
- Border Biomedical Research Center and Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
| | - Armando Varela-Ramirez
- Border Biomedical Research Center and Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
| | - Xiaolei Tang
- Department of Medicine, Loma Linda University, Loma Linda, California, United States of America
| | - Brenda Anchondo
- Border Biomedical Research Center and Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
| | - Diego Magallanes
- Border Biomedical Research Center and Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
| | - Renato J. Aguilera
- Border Biomedical Research Center and Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
- * E-mail:
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Song Y, Giske CG, Gille-Johnson P, Emanuelsson O, Lundeberg J, Gyarmati P. Nuclease-assisted suppression of human DNA background in sepsis. PLoS One 2014; 9:e103610. [PMID: 25076135 PMCID: PMC4116218 DOI: 10.1371/journal.pone.0103610] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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: 04/30/2014] [Accepted: 06/29/2014] [Indexed: 11/18/2022] Open
Abstract
Sepsis is a severe medical condition characterized by a systemic inflammatory response of the body caused by pathogenic microorganisms in the bloodstream. Blood or plasma is typically used for diagnosis, both containing large amount of human DNA, greatly exceeding the DNA of microbial origin. In order to enrich bacterial DNA, we applied the C0t effect to reduce human DNA background: a model system was set up with human and Escherichia coli (E. coli) DNA to mimic the conditions of bloodstream infections; and this system was adapted to plasma and blood samples from septic patients. As a consequence of the C0t effect, abundant DNA hybridizes faster than rare DNA. Following denaturation and re-hybridization, the amount of abundant DNA can be decreased with the application of double strand specific nucleases, leaving the non-hybridized rare DNA intact. Our experiments show that human DNA concentration can be reduced approximately 100,000-fold without affecting the E. coli DNA concentration in a model system with similarly sized amplicons. With clinical samples, the human DNA background was decreased 100-fold, as bacterial genomes are approximately 1,000-fold smaller compared to the human genome. According to our results, background suppression can be a valuable tool to enrich rare DNA in clinical samples where a high amount of background DNA can be found.
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Affiliation(s)
- Yajing Song
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Christian G. Giske
- Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- Karolinska University Hospital, Department of Clinical Microbiology, Stockholm, Sweden
| | - Patrik Gille-Johnson
- Division of Infectious Diseases, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Olof Emanuelsson
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Joakim Lundeberg
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Peter Gyarmati
- Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
- Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- Karolinska University Hospital, Department of Clinical Microbiology, Stockholm, Sweden
- * E-mail:
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48
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Sato S, Takenaka S. Highly sensitive nuclease assays based on chemically modified DNA or RNA. Sensors (Basel) 2014; 14:12437-50. [PMID: 25019631 PMCID: PMC4168492 DOI: 10.3390/s140712437] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/25/2014] [Accepted: 07/09/2014] [Indexed: 02/06/2023]
Abstract
Nucleolytic enzymes are associated with various diseases, and several methods have been developed for their detection. DNase expression is modulated in such diseases as acute myocardial infarction, transient myocardial ischemia, oral cancer, stomach cancer, and malignant lymphoma, and DNase I is used in cystic fibroma therapy. RNase is used to treat mesothelial cancer because of its antiproliferative, cytotoxic, and antineoplastic activities. Angiogenin, an angiogenic factor, is a member of the RNase A family. Angiogenin inhibitors are being developed as anticancer drugs. In this review, we describe fluorometric and electrochemical techniques for detecting DNase and RNase in disease. Oligonucleotides having fluorescence resonance energy transfer (FRET)-causing chromophores are non-fluorescent by themselves, yet become fluorescent upon cleavage by DNase or RNase. These oligonucleotides serve as a powerful tool to detect activities of these enzymes and provide a basis for drug discovery. In electrochemical techniques, ferrocenyl oligonucleotides with or without a ribonucleoside unit are used for the detection of RNase or DNase. This technique has been used to monitor blood or serum samples in several diseases associated with DNase and RNase and is unaffected by interferents in these sample types.
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Affiliation(s)
- Shinobu Sato
- Department of Applied Chemistry and Research Center for Bio-Microsensing Technology, Kyushu Institute of Technology, Kitakyushu, Fukuoka 804-8550, Japan.
| | - Shigeori Takenaka
- Department of Applied Chemistry and Research Center for Bio-Microsensing Technology, Kyushu Institute of Technology, Kitakyushu, Fukuoka 804-8550, Japan.
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49
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Landry KS, Levin RE. Characterization of a recently purified thermophilic DNase from a novel thermophilic fungus. Appl Biochem Biotechnol 2014; 173:1587-96. [PMID: 24952219 DOI: 10.1007/s12010-014-0907-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 01/28/2014] [Accepted: 04/03/2014] [Indexed: 11/28/2022]
Abstract
A newly isolated thermophilic fungus was found to produce a partially inducible extracellular DNase. This manuscript focuses on the characterization of this novel thermophilic DNase in terms of optimal enzyme conditions, molecular weight, and certain kinetic properties. The DNase was found to be inactivated by the presence of EDTA demonstrating its dependence on metal cofactors for activity. Maximum activity occurred at pH 6.0 with no activity at pH 2.0 or 10.0. The optimal temperature for the purified DNase was 65 °C. The thermophilic DNase was found to be an exonuclease with an estimated molecular weight of 56 kDa.
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Affiliation(s)
- Kyle S Landry
- Department of Food Science, Massachusetts Agricultural Experiment Station, University of Massachusetts, Amherst, MA, 01003, USA,
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50
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Rumi MAK, Dhakal P, Kubota K, Chakraborty D, Lei T, Larson MA, Wolfe MW, Roby KF, Vivian JL, Soares MJ. Generation of Esr1-knockout rats using zinc finger nuclease-mediated genome editing. Endocrinology 2014; 155:1991-9. [PMID: 24506075 PMCID: PMC3990838 DOI: 10.1210/en.2013-2150] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Estrogens play pivotal roles in development and function of many organ systems, including the reproductive system. We have generated estrogen receptor 1 (Esr1)-knockout rats using zinc finger nuclease (ZFN) genome targeting. mRNAs encoding ZFNs targeted to exon 3 of Esr1 were microinjected into single-cell rat embryos and transferred to pseudopregnant recipients. Of 17 live births, 5 had biallelic and 1 had monoallelic Esr1 mutations. A founder with monoallelic mutations was backcrossed to a wild-type rat. Offspring possessed only wild-type Esr1 alleles or wild-type alleles and Esr1 alleles containing either 482 bp (Δ482) or 223 bp (Δ223) deletions, indicating mosaicism in the founder. These heterozygous mutants were bred for colony expansion, generation of homozygous mutants, and phenotypic characterization. The Δ482 Esr1 allele yielded altered transcript processing, including the absence of exon 3, aberrant splicing of exon 2 and 4, and a frameshift that generated premature stop codons located immediately after the codon for Thr157. ESR1 protein was not detected in homozygous Δ482 mutant uteri. ESR1 disruption affected sexually dimorphic postnatal growth patterns and serum levels of gonadotropins and sex steroid hormones. Both male and female Esr1-null rats were infertile. Esr1-null males had small testes with distended and dysplastic seminiferous tubules, whereas Esr1-null females possessed large polycystic ovaries, thread-like uteri, and poorly developed mammary glands. In addition, uteri of Esr1-null rats did not effectively respond to 17β-estradiol treatment, further demonstrating that the Δ482 Esr1 mutation created a null allele. This rat model provides a new experimental tool for investigating the pathophysiology of estrogen action.
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MESH Headings
- Animals
- Codon, Nonsense
- Crosses, Genetic
- Deoxyribonucleases/chemistry
- Deoxyribonucleases/genetics
- Deoxyribonucleases/metabolism
- Estrogen Receptor alpha/chemistry
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Exons
- Female
- Gene Knockout Techniques
- Infertility, Female/blood
- Infertility, Female/metabolism
- Infertility, Female/pathology
- Infertility, Male/blood
- Infertility, Male/metabolism
- Infertility, Male/pathology
- Male
- Microinjections
- Protein Engineering
- RNA, Messenger/metabolism
- Rats
- Rats, Mutant Strains
- Rats, Sprague-Dawley
- Rats, Transgenic
- Zinc Fingers
- Zygote/metabolism
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Affiliation(s)
- M A Karim Rumi
- Institute for Reproductive Health and Regenerative Medicine; Departments of Pathology and Laboratory Medicine (M.A.K.R., P.D., K.K., D.C., T.L., J.L.V., M.J.S.), Molecular and Integrative Physiology (M.A.L., M.W.W.), and Anatomy and Cell Biology (K.F.R.), University of Kansas Medical Center, Kansas City, Kansas 66160
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