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Baglivo I, Malgieri G, Roop RM, Barton IS, Wang X, Russo V, Pirone L, Pedone EM, Pedone PV. MucR protein: Three decades of studies have led to the identification of a new H-NS-like protein. Mol Microbiol 2024. [PMID: 38619026 DOI: 10.1111/mmi.15261] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/16/2024]
Abstract
MucR belongs to a large protein family whose members regulate the expression of virulence and symbiosis genes in α-proteobacteria species. This protein and its homologs were initially studied as classical transcriptional regulators mostly involved in repression of target genes by binding their promoters. Very recent studies have led to the classification of MucR as a new type of Histone-like Nucleoid Structuring (H-NS) protein. Thus this review is an effort to put together a complete and unifying story demonstrating how genetic and biochemical findings on MucR suggested that this protein is not a classical transcriptional regulator, but functions as a novel type of H-NS-like protein, which binds AT-rich regions of genomic DNA and regulates gene expression.
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Affiliation(s)
- Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Roy Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ian S Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Emilia M Pedone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
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2
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Shi D, Huang Y, Bai C. Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases. Polymers (Basel) 2023; 15:polym15071763. [PMID: 37050377 PMCID: PMC10096840 DOI: 10.3390/polym15071763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein–DNA complex, its structural and dynamic features have been successively revealed in recent years. However, its regulatory mechanism, which is modulated by multiple factors, still requires systemic discussion. This study summarizes the regulatory factors of the nucleosome’s dynamic features from the perspective of histone modification, DNA methylation, and the nucleosome-interacting factors (transcription factors and nucleosome-remodeling proteins and cations) and focuses on the research exploring the molecular mechanism through both computational and experimental approaches. The regulatory factors that affect the dynamic features of nucleosomes are also discussed in detail, such as unwrapping, wrapping, sliding, and stacking. Due to the complexity of the high-order topological structures of nucleosomes and the comprehensive effects of regulatory factors, the research on the functional modulation mechanism of nucleosomes has encountered great challenges. The integration of computational and experimental approaches, the construction of physical modes for nucleosomes, and the application of deep learning techniques will provide promising opportunities for further exploration.
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Affiliation(s)
- Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Yuxin Huang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- Chenzhu (MoMeD) Biotechnology Co., Ltd., Hangzhou 310005, China
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3
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Kanu GA, Parambath JBM, Abu Odeh RO, Mohamed AA. Gold Nanoparticle-Mediated Gene Therapy. Cancers (Basel) 2022; 14:5366. [PMID: 36358785 PMCID: PMC9653658 DOI: 10.3390/cancers14215366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 07/30/2023] Open
Abstract
Gold nanoparticles (AuNPs) have gained increasing attention as novel drug-delivery nanostructures for the treatment of cancers, infections, inflammations, and other diseases and disorders. They are versatile in design, synthesis, modification, and functionalization. This has many advantages in terms of gene editing and gene silencing, and their application in genetic illnesses. The development of several techniques such as CRISPR/Cas9, TALEN, and ZFNs has raised hopes for the treatment of genetic abnormalities, although more focused experimentation is still needed. AuNPs, however, have been much more effective in trending research on this subject. In this review, we highlight recently well-developed advancements that are relevant to cutting-edge gene therapies, namely gene editing and gene silencing in diseases caused by a single gene in humans by taking an edge of the unique properties of the AuNPs, which will be an important outlook for future research.
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Affiliation(s)
- Gayathri A. Kanu
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Javad B. M. Parambath
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Center for Advanced Materials Research, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Raed O. Abu Odeh
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Ahmed A. Mohamed
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Center for Advanced Materials Research, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah 27272, United Arab Emirates
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Zhang M, Current JZ, Chaney HL, Yao J. Identification of the DNA binding element of ZNFO, an oocyte-specific zinc finger transcription factor in cattle. Gene 2022; 834:146655. [PMID: 35680024 DOI: 10.1016/j.gene.2022.146655] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/14/2022] [Accepted: 06/02/2022] [Indexed: 11/04/2022]
Abstract
The maternal effect genes are essential components of oocyte competence, which orchestrate the early developmental events before zygotic genome activation (ZGA). The Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KRAB-ZFPs) constitute the largest transcription factor family in mammals. As a novel maternal effect gene, ZNFO was identified previously in our laboratory. The gene codes for a KRAB-ZFP specifically expressed in bovine oocytes and early embryos and gene silencing experiments have demonstrated that ZNFO is required for early embryonic development in cattle. In the present study, we identified a consensus sequence, ATATCCTGTTTAAACCCC, as the DNA binding element of ZNFO (ZNFOBE) using a library of random oligonucleotides by cyclic amplification of sequence target (CAST) analysis. Sequence-specific binding of ZNFO to the DNA binding element was confirmed by an electrophoretic mobility shift assay (EMSA), and the key nucleotides in the ZNFOBE that are required for specific binding by ZNFO were further determined by a competitive EMSA using mutant competitors. Through a luciferase-based reporter assay, it was confirmed that the interaction between ZNFO and ZNFOBE is required for the repressive function of ZNFO. These results provide an essential step towards the identification of ZNFO regulated genes that play important roles during early embryonic development.
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Affiliation(s)
- Mingxiang Zhang
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Jaelyn Z Current
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Heather L Chaney
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Jianbo Yao
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
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Neuhaus D. Zinc finger structure determination by NMR: Why zinc fingers can be a handful. Prog Nucl Magn Reson Spectrosc 2022; 130-131:62-105. [PMID: 36113918 PMCID: PMC7614390 DOI: 10.1016/j.pnmrs.2022.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/09/2022] [Accepted: 07/10/2022] [Indexed: 06/07/2023]
Abstract
Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.
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Affiliation(s)
- David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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Abstract
DNA-protein interactions regulate several biophysical functions, yet the mechanism of only a few is investigated in molecular detail. An important example is the intercalation of transcription factor proteins into DNA that produce bent and kinked DNA. Here, we have studied the molecular mechanism of the intercalation of a transcription factor SOX4 into DNA with a goal to understand the sequence of molecular events that precede the bending and kinking of the DNA. Our long well-tempered metadynamics and molecular dynamics (MD) simulations show that the protein primarily binds to the backbone of DNA and rotates around it to form an intercalative native state. We show that although there are multiple pathways for intercalation, the deintercalation pathway matches with the most probable intercalation pathway. In both cases, bending and kinking happen simultaneously, driven by the onset of the intercalation of the amino acid.
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Affiliation(s)
- Reman Kumar Singh
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
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7
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Chen Y, Yuan S, Liu Y, Huang G. Rapid desalting during electrospray ionization mass spectrometry for investigating protein-ligand interactions in the presence of concentrated salts. Anal Chim Acta 2021; 1141:120-126. [PMID: 33248644 DOI: 10.1016/j.aca.2020.10.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/19/2020] [Revised: 10/10/2020] [Accepted: 10/19/2020] [Indexed: 11/18/2022]
Abstract
Investigation of protein-ligand interactions in physiological conditions is crucial for better understanding of biochemistry because the binding stoichiometry and conformations of complexes in biological processes, such as various types of regulation and transportation, could reveal key pathways in organisms. Nanoelectrospray ionization mass spectrometry is widely used in studies of biological processes and systems biology. However, non-volatile salts in biological fluid may adversely interfere with nanoelectrospray ionization mass spectrometry. In this study, the previously developed method of induced nanoelectrospray ionization was used to facilitate in situ desalting of protein in solutions with high concentrations of non-volatile salts, and direct investigation of protein-ligand interactions for the first time. In situ desalting occurred at the tip of emitters within a short period lasting for a few to tens of milliseconds, enabling the maintenance of nativelike conditions compatible with mass spectrometry measurements. Induced nanoelectrospray ionization was driven by pulsed potential and exhibited microelectrophoresis effect in each spray cycle, which is not observed in conventional nanoelectrospray ionization because the continuous spray procedure is driven by direct current. Microelectrophoresis caused desalting through micron-sized spray emitters (1-20 μm), as confirmed experimentally with proteins in 100 mM NaCl solution. The method developed in this study has been further illustrated as a potential option for fast and direct identification of protein-ligand (small molecules or metal ions) interactions in complex samples. The results of this study demonstrate that the newly developed method may represent a reliable approach for investigations of proteins and protein complexes in biological samples.
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Affiliation(s)
- Yuting Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China
| | - Siming Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China
| | - Yangzhong Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China
| | - Guangming Huang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China; National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, 230029, PR China.
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8
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Ferreira D, Fontinha D, Martins C, Pires D, Fernandes AR, Baptista PV. Gold Nanoparticles for Vectorization of Nucleic Acids for Cancer Therapeutics. Molecules 2020; 25:E3489. [PMID: 32751935 PMCID: PMC7435825 DOI: 10.3390/molecules25153489] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 06/22/2020] [Revised: 07/25/2020] [Accepted: 07/28/2020] [Indexed: 01/26/2023] Open
Abstract
Cancer remains a complex medical challenge and one of the leading causes of death worldwide. Nanomedicines have been proposed as innovative platforms to tackle these complex diseases, where the combination of several treatment strategies might enhance therapy success. Among these nanomedicines, nanoparticle mediated delivery of nucleic acids has been put forward as key instrument to modulate gene expression, be it targeted gene silencing, interference RNA mechanisms and/or gene edition. These novel delivery systems have strongly relied on nanoparticles and, in particular, gold nanoparticles (AuNPs) have paved the way for efficient delivery systems due to the possibility to fine-tune their size, shape and surface properties, coupled to the ease of functionalization with different biomolecules. Herein, we shall address the different molecular tools for modulation of expression of oncogenes and tumor suppressor genes and discuss the state-of-the-art of AuNP functionalization for nucleic acid delivery both in vitro and in vivo models. Furthermore, we shall highlight the clinical applications of these spherical AuNP based conjugates for gene delivery, current challenges, and future perspectives in nanomedicine.
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Affiliation(s)
- Daniela Ferreira
- UCIBIO, Dept. of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - David Fontinha
- UCIBIO, Dept. of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Catarina Martins
- UCIBIO, Dept. of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - David Pires
- UCIBIO, Dept. of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Dept. of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Pedro V Baptista
- UCIBIO, Dept. of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
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9
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Padjasek M, Kocyła A, Kluska K, Kerber O, Tran JB, Krężel A. Structural zinc binding sites shaped for greater works: Structure-function relations in classical zinc finger, hook and clasp domains. J Inorg Biochem 2020; 204:110955. [DOI: 10.1016/j.jinorgbio.2019.110955] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/08/2019] [Accepted: 12/01/2019] [Indexed: 12/12/2022]
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10
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Li H, Yang Y, Hong W, Huang M, Wu M, Zhao X. Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects. Signal Transduct Target Ther 2020; 5:1. [PMID: 32296011 PMCID: PMC6946647 DOI: 10.1038/s41392-019-0089-y] [Citation(s) in RCA: 842] [Impact Index Per Article: 210.5] [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: 09/14/2019] [Revised: 09/21/2019] [Accepted: 09/21/2019] [Indexed: 02/06/2023] Open
Abstract
Based on engineered or bacterial nucleases, the development of genome editing technologies has opened up the possibility of directly targeting and modifying genomic sequences in almost all eukaryotic cells. Genome editing has extended our ability to elucidate the contribution of genetics to disease by promoting the creation of more accurate cellular and animal models of pathological processes and has begun to show extraordinary potential in a variety of fields, ranging from basic research to applied biotechnology and biomedical research. Recent progress in developing programmable nucleases, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas-associated nucleases, has greatly expedited the progress of gene editing from concept to clinical practice. Here, we review recent advances of the three major genome editing technologies (ZFNs, TALENs, and CRISPR/Cas9) and discuss the applications of their derivative reagents as gene editing tools in various human diseases and potential future therapies, focusing on eukaryotic cells and animal models. Finally, we provide an overview of the clinical trials applying genome editing platforms for disease treatment and some of the challenges in the implementation of this technology.
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Affiliation(s)
- Hongyi Li
- Department of Gynecology and Obstetrics, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Yang Yang
- Department of Gynecology and Obstetrics, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Weiqi Hong
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P. R. China
| | - Mengyuan Huang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P. R. China
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, 58203, USA.
| | - Xia Zhao
- Department of Gynecology and Obstetrics, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, 610041, P. R. China.
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12
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Watanabe T. Evolution of the neural sex-determination system in insects: does fruitless homologue regulate neural sexual dimorphism in basal insects? Insect Mol Biol 2019; 28:807-827. [PMID: 31066110 DOI: 10.1111/imb.12590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the brain of holometabolous insects such as the fruit fly Drosophila melanogaster, the fruitless gene produces sex-specific gene products under the control of the sex-specific splicing cascade and contributes to the formation of the sexually dimorphic circuits. Similar sex-specific gene products of fruitless homologues have been identified in other holometabolous insects such as mosquitoes and a parasitic wasp, suggesting the fruitless-dependent neural sex-determination system is widely conserved amongst holometabolous insects. However, it remains obscure whether the fruitless-dependent neural sex-determination system is present in basal hemimetabolous insects. To address this issue, identification, characterization, and expression analyses of the fruitless homologue were conducted in the two-spotted cricket, Gryllus bimaculatus, as a model hemimetabolous insect. The Gryllus fruitless gene encodes multiple isoforms with a unique zinc finger domain, and does not encode a sex-specific gene product. The Gryllus Fruitless protein is broadly expressed in the neurones and glial cells in the brain, and there was no prominent sex-related difference in the expression levels of Gryllus fruitless isoforms. The results suggest that the Gryllus fruitless gene is not involved in the neural sex-determination in the cricket brain.
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Affiliation(s)
- T Watanabe
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
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13
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Bao SJ, Liu CY, Zhang M, Chen XR, Yu H, Li HX, Braunstein P, Lang JP. Metal complexes with the zwitterion 4-(trimethylammonio)benzenethiolate: Synthesis, structures and applications. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Chirgadze YN, Ivanov VV. Binding of Cys2His2 transcription factors with operator DNA: functional role of linkers between Zn-fingers. J Biomol Struct Dyn 2019; 38:3736-3742. [PMID: 31448692 DOI: 10.1080/07391102.2019.1659857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yuri N Chirgadze
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Victor V Ivanov
- Joint Institute for Nuclear Research, Dubna, Russia.,National Research Nuclear University MEPhI, Moscow, Russia
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15
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Liu B, Liu Y, Wang B, Luo Q, Shi J, Gan J, Shen WH, Yu Y, Dong A. The transcription factor OsSUF4 interacts with SDG725 in promoting H3K36me3 establishment. Nat Commun 2019; 10:2999. [PMID: 31278262 DOI: 10.1038/s41467-019-10850-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/04/2019] [Indexed: 12/18/2022] Open
Abstract
The different genome-wide distributions of tri-methylation at H3K36 (H3K36me3) in various species suggest diverse mechanisms for H3K36me3 establishment during evolution. Here, we show that the transcription factor OsSUF4 recognizes a specific 7-bp DNA element, broadly distributes throughout the rice genome, and recruits the H3K36 methyltransferase SDG725 to target a set of genes including the key florigen genes RFT1 and Hd3a to promote flowering in rice. Biochemical and structural analyses indicate that several positive residues within the zinc finger domain are vital for OsSUF4 function in planta. Our results reveal a regulatory mechanism contributing to H3K36me3 distribution in plants. The distribution of H3K36me3 varies between species. Here Liu et al. show that the OsSUF4 transcription factor binds its target motif via a zinc finger domain to promote H3K36 methyltransferase targeting close to the transcription start site of genes including the flowering regulators RFT1 and Hd3a.
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16
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Zhu M, Hu X, Liang Z, Jiang M, Xue R, Gong Y, Zhang X, Cao G, Gong C. Functional characterization of BmOVOs in silkworm, Bombyx mori. BMC Genomics 2019; 20:342. [PMID: 31060506 PMCID: PMC6503385 DOI: 10.1186/s12864-019-5697-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 04/15/2019] [Indexed: 01/07/2023] Open
Abstract
Background In our previous study, we identified four isoforms of the Bmovo gene, Bmovo-1, Bmovo-2, Bmovo-3 and Bmovo-4 from the silkworm ovary and verified that ovarian development was regulated by the BmOVO proteins. Results: To understand the regulatory mechanisms of ovarian development, the regulation of four BmOVO isoforms on the B. mori ovarian tumor (Bmotu) promoter activity was investigated with luciferase reporter assays. The results showed the Bmotu promoter activity was positively regulated by BmOVO-1, BmOVO-2, BmOVO-3 and BmOVO-4 in a dose-dependent manner, of which BmOVO-2 had the highest transcriptional activation. However, the first (A1) and third acidic domains (A3) at the N-terminus of BmOVO-1 are transcriptional repression domains, while the fourth (A4) and fifth acidic domains (A5) are transcriptional activation domains. A recombinant BmOVO zinc-finger domain was found to bind to the GTACCGTTGTA sequence located at the Bmotu promoter. Furthermore, the Bmotu promoter activity was negatively regulated by ‘Tal-like’ peptide, which can trigger BmOVO-1 degradation at the N-terminus. Conclusions These results will help us to further understand the regulatory mechanisms of BmOVO isoforms on Bmotu promoter activity and ovarian development in the silkworm. Electronic supplementary material The online version of this article (10.1186/s12864-019-5697-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Zhu
- School of Biology and Basic Medical Sciences, Soochow University, No.199 Ren'ai Road, Dushu Lake Higher Education Town, Suzhou Industrial Park, Suzhou, Jiangsu, 215123, People's Republic of China
| | - Xiaolong Hu
- School of Biology and Basic Medical Sciences, Soochow University, No.199 Ren'ai Road, Dushu Lake Higher Education Town, Suzhou Industrial Park, Suzhou, Jiangsu, 215123, People's Republic of China.,National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Zi Liang
- School of Biology and Basic Medical Sciences, Soochow University, No.199 Ren'ai Road, Dushu Lake Higher Education Town, Suzhou Industrial Park, Suzhou, Jiangsu, 215123, People's Republic of China
| | - Mengsheng Jiang
- School of Biology and Basic Medical Sciences, Soochow University, No.199 Ren'ai Road, Dushu Lake Higher Education Town, Suzhou Industrial Park, Suzhou, Jiangsu, 215123, People's Republic of China
| | - Renyu Xue
- School of Biology and Basic Medical Sciences, Soochow University, No.199 Ren'ai Road, Dushu Lake Higher Education Town, Suzhou Industrial Park, Suzhou, Jiangsu, 215123, People's Republic of China.,National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, 215123, Jiangsu, China.,Agricultural Biotechnology Research Institute, Agricultural biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China
| | - Yongchang Gong
- School of Biology and Basic Medical Sciences, Soochow University, No.199 Ren'ai Road, Dushu Lake Higher Education Town, Suzhou Industrial Park, Suzhou, Jiangsu, 215123, People's Republic of China
| | - Xing Zhang
- School of Biology and Basic Medical Sciences, Soochow University, No.199 Ren'ai Road, Dushu Lake Higher Education Town, Suzhou Industrial Park, Suzhou, Jiangsu, 215123, People's Republic of China
| | - Guangli Cao
- School of Biology and Basic Medical Sciences, Soochow University, No.199 Ren'ai Road, Dushu Lake Higher Education Town, Suzhou Industrial Park, Suzhou, Jiangsu, 215123, People's Republic of China. .,National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, 215123, Jiangsu, China. .,Agricultural Biotechnology Research Institute, Agricultural biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China.
| | - Chengliang Gong
- School of Biology and Basic Medical Sciences, Soochow University, No.199 Ren'ai Road, Dushu Lake Higher Education Town, Suzhou Industrial Park, Suzhou, Jiangsu, 215123, People's Republic of China. .,National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, 215123, Jiangsu, China. .,Agricultural Biotechnology Research Institute, Agricultural biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China.
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17
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Dong J, Li F, Gao F, Wei J, Lin Y, Zhang Y, Lou J, Liu G, Dong Y, Liu L, Liu H, Wang J, Gong W. Structure of tRNA-Modifying Enzyme TiaS and Motions of Its Substrate Binding Zinc Ribbon. J Mol Biol 2018; 430:4183-94. [PMID: 30121296 DOI: 10.1016/j.jmb.2018.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 08/02/2018] [Accepted: 08/07/2018] [Indexed: 12/28/2022]
Abstract
The accurate modification of the tRNAIle anticodon wobble cytosine 34 is critical for AUA decoding in protein synthesis. Archaeal tRNAIle2 cytosine 34 is modified with agmatine in the presence of ATP by TiaS (tRNAIle2 agmatidine synthetase). However, no structure of apo-form full-length TiaS is available currently. Here, the crystal structures of apo TiaS and a complex of TiaS-agmatine-AMPPCP-Mg are presented, with properly folded zinc ribbon and Cys4-zinc coordination identified. Compared with tRNAIle2-bound form, the architecture of apo TiaS shows a totally different conformation of zinc ribbon. Molecular dynamics simulations of the docking complex between free-state TiaS and tRNAIle2 suggest that zinc ribbon domain is capable of performing large-scale motions to sample substrate binding-competent conformation. Principle component analysis and normal mode analysis show consistent results about the relative directionality of functionally correlated zinc ribbon motions. Apo TiaS and TiaS-agmatine-AMPPCP-Mg/TiaS-AMPCPP-Mg complex structures capture two snapshots of the flexible ATP-Mg binding p2loop step-by-step stabilization. Research from this study provides new insight into TiaS functional mechanism and the dynamic feature of zinc ribbons.
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18
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Hu P, Meng Z, Jia Y. Molecular characterization and quantification of estrogen receptors in turbot (Scophthalmus maximus). Gen Comp Endocrinol 2018; 257:38-49. [PMID: 28087301 DOI: 10.1016/j.ygcen.2017.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/22/2016] [Accepted: 01/02/2017] [Indexed: 01/11/2023]
Abstract
Estrogens regulate various reproductive processes via estrogen receptor (ER)-mediated signaling pathway in vertebrates. In this study, full-length sequences coding for ERα, ERβ1 and ERβ2 were isolated from female turbot (Scophthalmus maximus) by homology cloning and a strategy based on rapid amplification of cDNA end-polymerase chain reaction (RACE-PCR). The nucleotide and amino acid sequences of turbot ERs showed high homologies with the corresponding sequences of other fish species and significant homology with the Japanese flounder (Paralichthys olivaceus) and the European sea bass (Dicentrarchus labrax). Turbot ERs contained six typical nuclear receptor-characteristic domains and exhibited high evolutionary conservation in the functional domains. Quantitative real-time polymerase chain reaction analysis revealed that the erα and erβ (β1, β2) mRNAs were abundant in the liver and ovary, respectively. Furthermore, hepatic mRNA levels of erα and vitellogenin (vtg) were found increased gradually from pre-vitellogenesis to late-vitellogenesis stages, with the highest values observed at the late-vitellogenesis stage, and then decreased from migratory-nucleus to atresia stages. However, mRNA levels of erα in the ovary remained unchanged during ovarian development. Hepatosomatic index, gonadosomatic index, serum estradiol-17β and the mRNA levels of erβ1 and erβ2 in the ovary manifested results similar to the expression of erα mRNAs in the liver. These findings indicated that ERα is mainly involved in hepatic vitellogenesis, and ERβs may play crucial roles to regulate ovarian development in turbot. Overall, this study improves understanding of the physiological functions of turbot ERs, which will be valuable for fish reproduction and broodstock management.
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Affiliation(s)
- Peng Hu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao 266071, China
| | - Zhen Meng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao 266071, China
| | - Yudong Jia
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao 266071, China.
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19
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Abstract
The completion of genome, epigenome, and transcriptome mapping in multiple cell types has created a demand for precision biomolecular tools that allow researchers to functionally manipulate DNA, reconfigure chromatin structure, and ultimately reshape gene expression patterns. Epigenetic editing tools provide the ability to interrogate the relationship between epigenetic modifications and gene expression. Importantly, this information can be exploited to reprogram cell fate for both basic research and therapeutic applications. Three different molecular platforms for epigenetic editing have been developed: zinc finger proteins (ZFs), transcription activator-like effectors (TALEs), and the system of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins. These platforms serve as custom DNA-binding domains (DBDs), which are fused to epigenetic modifying domains to manipulate epigenetic marks at specific sites in the genome. The addition and/or removal of epigenetic modifications reconfigures local chromatin structure, with the potential to provoke long-lasting changes in gene transcription. Here we summarize the molecular structure and mechanism of action of ZF, TALE, and CRISPR platforms and describe their applications for the locus-specific manipulation of the epigenome. The advantages and disadvantages of each platform will be discussed with regard to genomic specificity, potency in regulating gene expression, and reprogramming cell phenotypes, as well as ease of design, construction, and delivery. Finally, we outline potential applications for these tools in molecular biology and biomedicine and identify possible barriers to their future clinical implementation.
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Affiliation(s)
- Charlene Babra Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
| | - Colette Moses
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Mahira Arooj
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia.
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia.
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20
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Chou CC, Wei SY, Lou YC, Chen C. In-depth study of DNA binding of Cys2His2 finger domains in testis zinc-finger protein. PLoS One 2017; 12:e0175051. [PMID: 28384299 DOI: 10.1371/journal.pone.0175051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/20/2017] [Indexed: 11/26/2022] Open
Abstract
Previously, we identified that both fingers 1 and 2 in the three Cys2His2 zinc-finger domains (TZD) of testis zinc-finger protein specifically bind to its cognate DNA; however, finger 3 is non-sequence–specific. To gain insights into the interaction mechanism, here we further investigated the DNA-binding characteristics of TZD bound to non-specific DNAs and its finger segments bound to cognate DNA. TZD in non-specific DNA binding showed smaller chemical shift perturbations, as expected. However, the direction of shift perturbation, change of DNA imino-proton NMR signal, and dynamics on the 15N backbone atom significantly differed between specific and non-specific binding. Using these unique characteristics, we confirmed that the three single-finger segments (TZD1, TZD2 and TZD3) and the two-finger segment (TZD23) non-specifically bind to the cognate DNA. In comparison, the other two-finger segment (TZD12) binding to the cognate DNA features simultaneous non-specific and semi-specific binding, both slowly exchanged in terms of NMR timescale. The process of TZD binding to the cognate DNA is likely stepwise: initially TZD non-specifically binds to DNA, then fingers 1 and 2 insert cooperatively into the major groove of DNA by semi-specific binding, and finally finger 3 non-specifically binds to DNA, which promotes the specific binding on fingers 1 and 2 and stabilizes the formation of a specific TZD–DNA complex.
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21
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Hu JH, Davis KM, Liu DR. Chemical Biology Approaches to Genome Editing: Understanding, Controlling, and Delivering Programmable Nucleases. Cell Chem Biol 2016; 23:57-73. [PMID: 26933736 DOI: 10.1016/j.chembiol.2015.12.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 12/28/2015] [Accepted: 12/29/2015] [Indexed: 12/15/2022]
Abstract
Programmable DNA nucleases have provided scientists with the unprecedented ability to probe, regulate, and manipulate the human genome. Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeat-Cas9 system (CRISPR-Cas9) represent a powerful array of tools that can bind to and cleave a specified DNA sequence. In their canonical forms, these nucleases induce double-strand breaks at a DNA locus of interest that can trigger cellular DNA repair processes that disrupt or replace genes. The fusion of these programmable nucleases with a variety of other protein domains has led to a rapidly growing suite of tools for activating, repressing, visualizing, and modifying loci of interest. Maximizing the usefulness and therapeutic relevance of these tools, however, requires precisely controlling their activity and specificity to minimize potentially toxic side effects arising from off-target activities. This need has motivated the application of chemical biology principles and methods to genome-editing proteins, including the engineering of variants of these proteins with improved or altered specificities, and the development of genetic, chemical, optical, and protein delivery methods that control the activity of these agents in cells. Advancing the capabilities, safety, effectiveness, and therapeutic relevance of genome-engineering proteins will continue to rely on chemical biology strategies that manipulate their activity, specificity, and localization.
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22
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Malgieri G, Palmieri M, Russo L, Fattorusso R, Pedone PV, Isernia C. The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart. FEBS J 2015; 282:4480-96. [PMID: 26365095 DOI: 10.1111/febs.13503] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/23/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
Classical zinc finger (ZF) domains were thought to be confined to the eukaryotic kingdom until the transcriptional regulator Ros protein was identified in Agrobacterium tumefaciens. The Ros Cys2 His2 ZF binds DNA in a peculiar mode and folds in a domain significantly larger than its eukaryotic counterpart consisting of 58 amino acids (the 9-66 region) arranged in a βββαα topology, and stabilized by a conserved, extensive, 15-residue hydrophobic core. The prokaryotic ZF domain, then, shows some intriguing new features that make it interestingly different from its eukaryotic counterpart. This review will focus on the prokaryotic ZFs, summarizing and discussing differences and analogies with the eukaryotic domains and providing important insights into their structure/function relationships.
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Affiliation(s)
- Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
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23
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Xu H, Zhou C, Zhang AK, Li W, Zhang J, Li K. A Mutagenesis Assay for Reporter Gene Screening Using Partially Degenerate Oligonucleotides of the Tandems NNT and NNC. Biomed Res Int 2015; 2015:950873. [PMID: 26167508 DOI: 10.1155/2015/950873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/02/2015] [Indexed: 11/24/2022]
Abstract
Not all proteins are tolerable to mutations. Whether a specific protein can be a mutable target is of importance in the biotechnology and pharmaceutical industry. This study reported a novel mutagenesis assay using tandem NNT and NNC oligonucleotides to test the mutability of a candidate gene. These two tandem oligonucleotides avoid the risk of forming nonsense mutations and render flexibility of truncating or expanding the insertion size. As a reporter gene, ZeoR (zeocin resistance gene) was confirmed to have a high tolerance for mutagenesis by this new assay.
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24
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Chen S, Pu L, Xie F, Zou Z, Jiang Y, Han K, Wang Y, Zhang Z. Differential expression of three estrogen receptors mRNAs in tissues, growth development, embryogenesis and gametogenesis from large yellow croaker, Larimichthys crocea. Gen Comp Endocrinol 2015; 216:134-51. [PMID: 25863348 DOI: 10.1016/j.ygcen.2015.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 01/16/2015] [Accepted: 04/05/2015] [Indexed: 11/30/2022]
Abstract
The biological activity of estrogens in target organs is mainly mediated by estrogen receptors (ERs). Herein, we addressed the isolation and expression analysis of three nuclear estrogen receptors, namely LcERα, LcERβ1, and LcERβ2 from Larimichthys crocea by means of SMART-RACE, qRT-PCR, and in situ hybridization. Results in different tissues showed that both LcERα and LcERβ2 had the highest expression levels in female liver, followed by testis, but LcERβ1 expression level was significantly higher in testis and ovary than in other tissues. Expression of LcERα and LcERβ2 was significantly higher than LcERβ1 in female liver, and LcERβ2 was significantly higher than LcERα and LcERβ1 in male liver. Moreover, we analyzed the expression of LcERs in gonad and liver at three different growth stages during the same breeding season. Significant up-regulated expression of LcERα and LcERβ2 were found in female liver at 1000dph compared with at 270dph. The expression of LcERβ2 was prominently higher in male liver than LcERα, LcERβ1 and LcAR, while LcERβ1 was lower than other receptors in male and female liver at all the three stages. In ovary, LcERα at 270dph was lower than at 635dph and 1000dph, but had no significant change in testis. The two LcERβ subtypes and LcAR highly expressed in the early testis, and gradually decrease with the development of testis. In embryogenesis, a significant increase in the expression of LcERα and LcERβ2 were observed after appearance of optic vesicles phase (11.8hpf). LcERβ1 gradually decrease with the embryogenesis but increased dramatically at 1dph. Results of in situ hybridization showed that signals of LcERα and LcERβ1 mRNA were mainly detected in Stage I-Stage IV oocytes, as well as in follicle cells around the Stage II-Stage IV and degenerated oocytes. Signals of LcERβ2 were detected in the cytoplasm of Stage I and Stage II oocytes but not in the follicle cells of all oocytes stages. In parallel, LcERα and LcERβ1 were detected in all cell types of spermatogenesis, but in terms of LcERβ2, little or no signals were detected during spermatogenesis. Based on these results, we deduced that both LcERα and LcERβ2 play a major role in mediating the physiological effects of estrogen in female liver, and LcERβ2 maybe also play an important role in regulation of vitellogenesis in male liver. Differential expression of LcERs and LcAR imply their physiological functions during development and differentiation of gonad. The signals for LcERα and LcERβ1 in follicle cells suggested that the follicle cell maybe an important site of estrogen action, by which estrogens exert influences on the maturation oocytes and ovulation. Furthermore, the steroid hormones produced by follicle cells may be related to the differential distributions among ER subtypes. Besides, we deduced that LcERα and LcERβ1 rather than LcERβ2 may play a major role in spermatogenesis of croaker. However, the differential expression of LcERβ2 during gametogenesis also implicates its certain functions in mediating physiological process of estrogen action.
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Affiliation(s)
- Shihai Chen
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China
| | - Lulu Pu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China
| | - Fangjing Xie
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China
| | - Zhihua Zou
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China
| | - Yonghua Jiang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China
| | - Kunhuang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Large Yellow Croaker, Ningde Fufa Fisheries Company Limited, Ningde 352103, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China.
| | - Ziping Zhang
- Department of Natural Sciences and Mathematics, State University of New York at Cobleskill, NY 12043, United States.
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25
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Tochio N, Umehara T, Nakabayashi K, Yoneyama M, Tsuda K, Shirouzu M, Koshiba S, Watanabe S, Kigawa T, Sasazuki T, Shirasawa S, Yokoyama S. Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT. ACTA ACUST UNITED AC 2015; 16:55-65. [PMID: 25801860 PMCID: PMC4427657 DOI: 10.1007/s10969-015-9196-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 03/12/2015] [Indexed: 11/28/2022]
Abstract
ZFAT is a transcriptional regulator, containing eighteen C2H2-type zinc-fingers and one AT-hook, involved in autoimmune thyroid disease, apoptosis, and immune-related cell survival. We determined the solution structures of the thirteen individual ZFAT zinc-fingers (ZF) and the tandemly arrayed zinc-fingers in the regions from ZF2 to ZF5, by NMR spectroscopy. ZFAT has eight uncommon bulged-out helix-containing zinc-fingers, and six of their structures (ZF4, ZF5, ZF6, ZF10, ZF11, and ZF13) were determined. The distribution patterns of the putative DNA-binding surface residues are different among the ZFAT zinc-fingers, suggesting the distinct DNA sequence preferences of the N-terminal and C-terminal zinc-fingers. Since ZFAT has three to five consecutive tandem zinc-fingers, which may cooperatively function as a unit, we also determined two tandemly arrayed zinc-finger structures, between ZF2 to ZF4 and ZF3 to ZF5. Our NMR spectroscopic analysis detected the interaction between ZF4 and ZF5, which are connected by an uncommon linker sequence, KKIK. The ZF4–ZF5 linker restrained the relative structural space between the two zinc-fingers in solution, unlike the other linker regions with determined structures, suggesting the involvement of the ZF4–ZF5 interfinger linker in the regulation of ZFAT function.
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Affiliation(s)
- Naoya Tochio
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,Department of Mathematical and Life Sciences, Research Center for the Mathematics on Chromatin Live Dynamics, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8530 Japan
| | - Takashi Umehara
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,PRESTO, Japan Science and Technology Agency (JST), 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, 157-8535 Japan
| | - Misao Yoneyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Kengo Tsuda
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Seizo Koshiba
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Satoru Watanabe
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Takanori Kigawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori, Yokohama, 226-8502 Japan.,RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Takehiko Sasazuki
- Institute for Advanced Studies, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8582 Japan
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180 Japan.,Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180 Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
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26
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Dutta S, Sundar D. Designing Zinc Finger Proteins for Applications in Synthetic Biology. Systems and Synthetic Biology 2015. [DOI: 10.1007/978-94-017-9514-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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27
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28
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Han G, Ferranco A, Feng X, Chen Z, Kraatz H. Synthesis, Characterization of Some Ferrocenoyl Cysteine and Histidine Conjugates, and Their Interactions with Some Metal Ions. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402470] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Guo‐Cheng Han
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin 541004, P. R. China, http://rsc.guet.edu.cn/RSC/public/show.aspx?par2=0014&par=864
| | - Annaleizle Ferranco
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada, http://www.utsc.utoronto.ca/~bkraatz/
| | - Xiao‐Zhen Feng
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin 541004, P. R. China, http://rsc.guet.edu.cn/RSC/public/show.aspx?par2=0014&par=864
| | - Zhencheng Chen
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin 541004, P. R. China, http://rsc.guet.edu.cn/RSC/public/show.aspx?par2=0014&par=864
| | - Heinz‐Bernhard Kraatz
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada, http://www.utsc.utoronto.ca/~bkraatz/
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29
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Park SY, Kim YG. Rapid Assembly and Cloning of Zinc Finger Proteins with Multiple Finger Modules. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.7.2197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Tripathy R, Kunwar PS, Sano H, Renault AD. Transcriptional regulation of Drosophila gonad formation. Dev Biol 2014; 392:193-208. [PMID: 24927896 DOI: 10.1016/j.ydbio.2014.05.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 05/22/2014] [Accepted: 05/26/2014] [Indexed: 01/08/2023]
Abstract
The formation of the Drosophila embryonic gonad, involving the fusion of clusters of somatic gonadal precursor cells (SGPs) and their ensheathment of germ cells, provides a simple and genetically tractable model for the interplay between cells during organ formation. In a screen for mutants affecting gonad formation we identified a SGP cell autonomous role for Midline (Mid) and Longitudinals lacking (Lola). These transcriptional factors are required for multiple aspects of SGP behaviour including SGP cluster fusion, germ cell ensheathment and gonad compaction. The lola locus encodes more than 25 differentially spliced isoforms and we have identified an isoform specific requirement for lola in the gonad which is distinct from that in nervous system development. Mid and Lola work in parallel in gonad formation and surprisingly Mid overexpression in a lola background leads to additional SGPs at the expense of fat body cells. Our findings support the idea that although the transcription factors required by SGPs can ostensibly be assigned to those being required for either SGP specification or behaviour, they can also interact to impinge on both processes.
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Affiliation(s)
- Ratna Tripathy
- Max Planck Institute for Developmental Biology, Spemannstr. 35, 72074 Tübingen, Germany
| | - Prabhat S Kunwar
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Hiroko Sano
- Department of Molecular Genetics, Institute of Life Sciences, Kurume University, Kurume, Fukuoka, Japan
| | - Andrew D Renault
- Max Planck Institute for Developmental Biology, Spemannstr. 35, 72074 Tübingen, Germany.
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Pröpper K, Meindl K, Sammito M, Dittrich B, Sheldrick GM, Pohl E, Usón I. Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries. Acta Crystallogr D Biol Crystallogr 2014; 70:1743-57. [PMID: 24914984 PMCID: PMC4051508 DOI: 10.1107/s1399004714007603] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [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: 10/18/2013] [Accepted: 04/04/2014] [Indexed: 11/11/2022]
Abstract
Protein-DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein-DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein-DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein-DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.
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Affiliation(s)
- Kevin Pröpper
- University of Göttingen, Germany
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
| | - Kathrin Meindl
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
| | - Massimo Sammito
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
| | | | | | | | - Isabel Usón
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
- Institucio Catalana de Recerca i Estudis Avancats (ICREA), Spain
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Gupta A, Christensen RG, Bell HA, Goodwin M, Patel RY, Pandey M, Enuameh MS, Rayla AL, Zhu C, Thibodeau-Beganny S, Brodsky MH, Joung JK, Wolfe SA, Stormo GD. An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins. Nucleic Acids Res 2014; 42:4800-12. [PMID: 24523353 PMCID: PMC4005693 DOI: 10.1093/nar/gku132] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [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: 12/05/2013] [Revised: 01/21/2014] [Accepted: 01/22/2014] [Indexed: 11/17/2022] Open
Abstract
Cys(2)-His(2) zinc finger proteins (ZFPs) are the largest family of transcription factors in higher metazoans. They also represent the most diverse family with regards to the composition of their recognition sequences. Although there are a number of ZFPs with characterized DNA-binding preferences, the specificity of the vast majority of ZFPs is unknown and cannot be directly inferred by homology due to the diversity of recognition residues present within individual fingers. Given the large number of unique zinc fingers and assemblies present across eukaryotes, a comprehensive predictive recognition model that could accurately estimate the DNA-binding specificity of any ZFP based on its amino acid sequence would have great utility. Toward this goal, we have used the DNA-binding specificities of 678 two-finger modules from both natural and artificial sources to construct a random forest-based predictive model for ZFP recognition. We find that our recognition model outperforms previously described determinant-based recognition models for ZFPs, and can successfully estimate the specificity of naturally occurring ZFPs with previously defined specificities.
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Affiliation(s)
- Ankit Gupta
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan G. Christensen
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Heather A. Bell
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Mathew Goodwin
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Ronak Y. Patel
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Manishi Pandey
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Metewo Selase Enuameh
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy L. Rayla
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Cong Zhu
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Stacey Thibodeau-Beganny
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael H. Brodsky
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - J. Keith Joung
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Scot A. Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Gary D. Stormo
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
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Kang M, Light K, Ai HW, Shen W, Kim CH, Chen PR, Lee HS, Solomon EI, Schultz PG. Evolution of iron(II)-finger peptides by using a bipyridyl amino acid. Chembiochem 2014; 15:822-825. [PMID: 24591102 DOI: 10.1002/cbic.201300727] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Indexed: 11/11/2022]
Abstract
We report the engineering of zinc-finger-like motifs containing the unnatural amino acid (2,2'-bipyridin-5-yl)alanine (Bpy-Ala). A phage-display library was constructed in which five residues in the N-terminal finger of zif268 were randomized to include both canonical amino acids and Bpy-Ala. Panning of this library against a nine-base-pair DNA binding site identified several Bpy-Ala-containing functional Zif268 mutants. These mutants bind the Zif268 recognition site with affinities comparable to that of the wild-type protein. Further characterization indicated that the mutant fingers bind low-spin Fe(II) rather than Zn(II) . This work demonstrates that an expanded genetic code can lead to new metal ion binding motifs that can serve as structural, catalytic, or regulatory elements in proteins.
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Affiliation(s)
- Mingchao Kang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037
| | - Kenneth Light
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford CA 94305
| | - Hui-Wang Ai
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037
| | - Weijun Shen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037
| | - Chan Hyuk Kim
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037
| | - Peng R Chen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037
| | - Hyun Soo Lee
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037
| | - Edward I Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford CA 94305
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037
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Zhang B, Xiang S, Yin Y, Gu L, Deng D. C-terminal in Sp1-like artificial zinc-finger proteins plays crucial roles in determining their DNA binding affinity. BMC Biotechnol 2013; 13:106. [PMID: 24289163 PMCID: PMC4219604 DOI: 10.1186/1472-6750-13-106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 11/25/2013] [Indexed: 11/17/2022] Open
Abstract
Background It is well known that the C-terminal zinc-finger-3 in transcription factor Sp1 contributes more than the N-terminal zinc-finger-1 in determining Sp1’s DNA binding capacity. Sp1-like artificial poly-zinc-finger proteins (ZFPs) are powerful biotechnological tools for gene-specific recognization and manipulation. It is important to understand whether the C-terminal fingers in the Sp1-like artificial ZFPs remain crucial for their DNA binding ability. Recently, a set of p16 promoter-specific seven-ZFPs (7ZFPs) has been constructed to reactivate the expression of methylation-silenced p16. These 7ZFPs contain one N-terminal three-zinc-finger domain of Sp1 (3ZF), two Sp1-like two-zinc-finger domains derived from the Sp1 finger-2 and finger-3 (2ZF) in the middle and C-terminal regions. Results In the present study, sets of variants for several representative 7ZFPs with the p16-binding affinity were further constructed. This was accomplished through finger replacements and key amino acid mutations in the N-terminal fingers, C-terminal fingers, and linker peptide, respectively. Their p16-binding activity was analysed using gel mobility shift assays. Results showed that the motif replacement or a key amino acid mutation (S > R) at position +2 of the α-helix in the C-terminal 2ZF domain completely abolished their p16-binding affinity. Deletion of three amino acids in a consensus linker (TGEKP > TG) between finger-7 and the 6 × Histidine-tag in the C-terminal also dramatically abolished their binding affinity. In contrast, the replacement of the finger-3 in the N-terminal 3ZF domain did not affect their binding affinity, but decreased their binding stability. Conclusions Altogether, the present study show that the C-terminal region may play crucial roles in determining the DNA binding affinity of Sp1-like artificial ZFPs.
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Affiliation(s)
| | | | | | | | - Dajun Deng
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China.
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Persikov AV, Rowland EF, Oakes BL, Singh M, Noyes MB. Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets. Nucleic Acids Res 2013; 42:1497-508. [PMID: 24214968 PMCID: PMC3919609 DOI: 10.1093/nar/gkt1034] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Cys2His2 zinc finger (ZF) is the most frequently found sequence-specific DNA-binding domain in eukaryotic proteins. The ZF's modular protein-DNA interface has also served as a platform for genome engineering applications. Despite decades of intense study, a predictive understanding of the DNA-binding specificities of either natural or engineered ZF domains remains elusive. To help fill this gap, we developed an integrated experimental-computational approach to enrich and recover distinct groups of ZFs that bind common targets. To showcase the power of our approach, we built several large ZF libraries and demonstrated their excellent diversity. As proof of principle, we used one of these ZF libraries to select and recover thousands of ZFs that bind several 3-nt targets of interest. We were then able to computationally cluster these recovered ZFs to reveal several distinct classes of proteins, all recovered from a single selection, to bind the same target. Finally, for each target studied, we confirmed that one or more representative ZFs yield the desired specificity. In sum, the described approach enables comprehensive large-scale selection and characterization of ZF specificities and should be a great aid in furthering our understanding of the ZF domain.
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Affiliation(s)
- Anton V Persikov
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Department of Computer Science, Princeton University, Princeton, NJ 08544, USA and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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Heffern MC, Kurutz JW, Meade TJ. Spectroscopic elucidation of the inhibitory mechanism of Cys2His2 zinc finger transcription factors by cobalt(III) Schiff base complexes. Chemistry 2013; 19:17043-53. [PMID: 24203451 DOI: 10.1002/chem.201301659] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 10/05/2013] [Indexed: 01/22/2023]
Abstract
Transcription factors are key regulators in both normal and pathological cell processes. Affecting the activity of these proteins is a promising strategy for understanding gene regulation and developing effective therapeutics. Co(III) Schiff base complexes ([Co(acacen)(L)2](+) where L=labile axial ligands) have been shown to be potent inhibitors of a number of zinc metalloproteins including Cys2His2 zinc finger transcription factors. Inhibition by [Co(acacen)(L)2](+) of the target protein is believed to occur through a dissociative exchange of the labile axial ligands for histidine (His) residues essential for function. Here, we report a series of spectroscopic investigations with model peptides of zinc fingers that elucidate the interaction between [Co(acacen)(L)2](+) complexes and zinc finger transcription factors. Observed changes in NMR chemical shifts and 2D (1)H-(1)H NOESY NMR spectra demonstrate the preference of [Co(acacen)(L)2](+) complexes to coordinate His residues over other amino acids. The conformation of [Co(acacen)(L)2](+) upon His coordination was characterized by (1)H NMR spectroscopy, near-UV CD, and electronic absorption. These studies reveal that the resulting His-coordinated [Co(acacen)(L)2](+) complex possesses an octahedral structure. The effects of [Co(acacen)(L)2](+) complexes on the zinc-finger structure were assessed by the degree of hydrogen bonding (probed by 2D NMR spectroscopy) and secondary-structure profiles measured by far-UV CD. These structural studies demonstrate the ability of [Co(acacen)(L)2](+) complexes to disrupt the ββα structure of zinc fingers, resulting in primarily random-coil conformations. A mechanism is described wherein [Co(acacen)(L)2](+) complexes inhibit zinc finger transcription factor activity through selectively coordinating His residues in the zinc finger by dissociative ligand exchange and disrupting the ββα structural motif required for gene regulation.
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Affiliation(s)
- Marie C Heffern
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Northwestern University, Evanston, Illinois 60208-3113 (USA)
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Esperón P, Scazzocchio C, Paulino M. In vitroandin silicoanalysis of theAspergillus nidulansDNA–CreA repressor interactions. J Biomol Struct Dyn 2013; 32:2033-41. [DOI: 10.1080/07391102.2013.843474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Abstract
Estrogens, steroid hormones critically involved in reproductive processes of vertebrates, signal primarily through their intracellular estrogen receptors (ERs). The ERs belong to a superfamily of nuclear receptors that act as ligand inducible transcription factors. Herein, we review what is known about ER structure, subtypes, mechanism(s) of action and auto-regulation by estrogens. Focus is placed on the ER in fish but comparisons are made to mammals and other vertebrates. Finally, we provide context and a proposed model integrating our knowledge on autoregulation of the receptor and its functions in the liver. Future areas of study are suggested, along with cautions when designing experiments, especially for the detection of endocrine disruptors.
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Affiliation(s)
- Erik R Nelson
- Pharmacology and Cancer Biology, Duke University School of Medicine, LSRC Bldg, Research Drive, Durham, NC 27710, United States.
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Corkins ME, May M, Ehrensberger KM, Hu YM, Liu YH, Bloor SD, Jenkins B, Runge KW, Bird AJ. Zinc finger protein Loz1 is required for zinc-responsive regulation of gene expression in fission yeast. Proc Natl Acad Sci U S A 2013; 110:15371-6. [PMID: 24003116 DOI: 10.1073/pnas.1300853110] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In Schizosaccharomyces pombe, alcohol dehydrogenase 1 (Adh1) is an abundant zinc-requiring enzyme that catalyses the conversion of acetaldehyde to ethanol during fermentation. In a zinc-replete cell, adh1 is highly expressed. However, in zinc-limited cells, adh1 gene expression is repressed, and cells induce the expression of an alternative alcohol dehydrogenase encoded by the adh4 gene. In our studies examining this zinc-dependent switch in alcohol dehydrogenase gene expression, we isolated an adh1Δ strain containing a partial loss of function mutation that resulted in higher levels of adh4 transcripts in zinc-replete cells. This mutation also led to the aberrant expression of other genes that are typically regulated by zinc. Using linkage analysis, we have mapped the position of this mutation to a single gene called Loss Of Zinc sensing 1 (loz1). Loz1 is a 55-kDa protein that contains a double C2H2-type zinc finger domain. The mapped mutation that disrupts Loz1 function leads to an arginine to glycine substitution in the second zinc finger domain, suggesting that the double zinc finger domain is important for Loz1 function. We show that loz1Δ cells hyperaccumulate zinc and that Loz1 is required for gene repression in zinc-replete cells. We also have found that Loz1 negatively autoregulates its own expression. We propose that Loz1 is a unique metalloregulatory factor that plays a central role in zinc homeostasis in S. pombe.
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Enuameh MS, Asriyan Y, Richards A, Christensen RG, Hall VL, Kazemian M, Zhu C, Pham H, Cheng Q, Blatti C, Brasefield JA, Basciotta MD, Ou J, McNulty JC, Zhu LJ, Celniker SE, Sinha S, Stormo GD, Brodsky MH, Wolfe SA. Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res 2013; 23:928-40. [PMID: 23471540 PMCID: PMC3668361 DOI: 10.1101/gr.151472.112] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have characterized the DNA-binding specificities of 129 zinc finger sets from Drosophila using a bacterial one-hybrid system. This data set contains the DNA-binding specificities for at least one encoded ZFP from 70 unique genes and 23 alternate splice isoforms representing the largest set of characterized ZFPs from any organism described to date. These recognition motifs can be used to predict genomic binding sites for these factors within the fruit fly genome. Subsets of fingers from these ZFPs were characterized to define their orientation and register on their recognition sequences, thereby allowing us to define the recognition diversity within this finger set. We find that the characterized fingers can specify 47 of the 64 possible DNA triplets. To confirm the utility of our finger recognition models, we employed subsets of Drosophila fingers in combination with an existing archive of artificial zinc finger modules to create ZFPs with novel DNA-binding specificity. These hybrids of natural and artificial fingers can be used to create functional zinc finger nucleases for editing vertebrate genomes.
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Affiliation(s)
- Metewo Selase Enuameh
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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Vandevenne M, Jacques DA, Artuz C, Nguyen CD, Kwan AHY, Segal DJ, Matthews JM, Crossley M, Guss JM, Mackay JP. New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217. J Biol Chem 2013; 288:10616-27. [PMID: 23436653 DOI: 10.1074/jbc.m112.441451] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Classical zinc fingers (ZFs) are one of the most abundant and best characterized DNA-binding domains. Typically, tandem arrays of three or more ZFs bind DNA target sequences with high affinity and specificity, and the mode of DNA recognition is sufficiently well understood that tailor-made ZF-based DNA-binding proteins can be engineered. We have shown previously that a two-zinc finger unit found in the transcriptional coregulator ZNF217 recognizes DNA but with an affinity and specificity that is lower than other ZF arrays. To investigate the basis for these differences, we determined the structure of a ZNF217-DNA complex. We show that although the overall position of the ZFs on the DNA closely resembles that observed for other ZFs, the side-chain interaction pattern differs substantially from the canonical model. The structure also reveals the presence of two methyl-π interactions, each featuring a tyrosine contacting a thymine methyl group. To our knowledge, interactions of this type have not previously been described in classical ZF-DNA complexes. Finally, we investigated the sequence specificity of this two-ZF unit and discuss how ZNF217 might discriminate its target DNA sites in the cell.
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Affiliation(s)
- Marylène Vandevenne
- School of Molecular Bioscience, University of Sydney, New South Wales, 2006 Australia
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Zheng AX, Si J, Tang XY, Miao LL, Yu M, Hou KP, Wang F, Li HX, Lang JP. Reactions of the Cationic Zinc Thiolate Model Complex [Zn(Tab)4](PF6)2 with N-Donor Ligands and Cobalt Dichloride. Inorg Chem 2012; 51:10262-73. [DOI: 10.1021/ic301191n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ai-Xia Zheng
- College of
Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s
Republic of China
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of
Organic Chemistry, Chinese Academy of Sciences, Shanghai 210093, People’s Republic of China
| | - Jing Si
- College of
Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s
Republic of China
| | - Xiao-Yan Tang
- Jiangsu Laboratory of Advanced Functional Materials, Changshu Institute of Technology, Changshu 215500,
People’s Republic of China
| | - Li-Li Miao
- College of
Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s
Republic of China
| | - Miao Yu
- College of
Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s
Republic of China
| | - Kai-Peng Hou
- College of
Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s
Republic of China
| | - Fan Wang
- College of
Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s
Republic of China
| | - Hong-Xi Li
- College of
Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s
Republic of China
| | - Jian-Ping Lang
- College of
Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s
Republic of China
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of
Organic Chemistry, Chinese Academy of Sciences, Shanghai 210093, People’s Republic of China
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Buck-Koehntop BA, Martinez-Yamout MA, Dyson HJ, Wright PE. Kaiso uses all three zinc fingers and adjacent sequence motifs for high affinity binding to sequence-specific and methyl-CpG DNA targets. FEBS Lett 2012; 586:734-9. [PMID: 22300642 DOI: 10.1016/j.febslet.2012.01.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [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: 09/15/2011] [Revised: 11/29/2011] [Accepted: 01/21/2012] [Indexed: 12/31/2022]
Abstract
Kaiso is a Cys(2)His(2) zinc finger (ZF) protein that mediates methyl-CpG-dependent and sequence-specific transcriptional repression. As a first step towards elucidating the structural and molecular basis for recognition of these disparate DNA sequences, the minimal binding region of Kaiso was identified and optimal DNA sequences for high-affinity interactions were characterized. Contrary to previous findings, Kaiso requires all three zinc fingers plus adjacent protein regions for DNA recognition. An N-terminal extension contributes to structural stability, while an extended C-terminal region augments DNA binding. Complexes formed between the optimized Kaiso construct and both DNA sequences are suitable for future structural evaluation.
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Affiliation(s)
- Bethany A Buck-Koehntop
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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45
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Prouse MB, Campbell MM. The interaction between MYB proteins and their target DNA binding sites. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2012; 1819:67-77. [DOI: 10.1016/j.bbagrm.2011.10.010] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 02/02/2023]
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46
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Wang Y, Zhu Y, Wang Y, Chen G. Structural analysis of zinc-finger (TTK) + [Cu(BPA)]2+ /[Cu(IDB)]2+ + DNA complexes: an investigation by molecular dynamics simulation. J Mol Recognit 2011; 24:981-94. [PMID: 22038805 DOI: 10.1002/jmr.1146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the present study, the molecular dynamics simulation technique is employed to investigate the hydrogen abstraction possibility from sugar of DNA in two designed complexes of copper-based chemical nuclease [Cu(BPA)](2+) bis(2-pyridylmethyl) amine (BPA) or [Cu(IDB)](2+) N,N-bis(2-benzimidazolylmethyl) amine (IDB) bound to the zinc finger protein Tramtrack (TTK). The simulated results show that each of the designed complexes can form a stable conformation within 30 ns of simulation time with the substrate OOH(-) and an 18-base pair (bp) DNA segment and is located in the major groove of the DNA segment. The active terminal O atom of the OOH(-) substrate is found in close proximity to the target C2'H, C3'H, C4'H or C5'H proton of the DNA in TTK + [Cu(BPA)OOH](+) + DNA or TTK + [Cu(IDB)OOH](+) + DNA complex, which is crucial to propose the hydrogen abstraction possibility that is responsible for the DNA cleavage. The positions of copper-based chemical nucleases bound to TTK may substantially influence the hydrogen abstraction possibility. The structures and sizes of ligands in copper-based nucleases are also found to have influence on the order of difficulty of the hydrogen abstraction from the sugars of DNA.
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Affiliation(s)
- Yaru Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
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47
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Hofstetter TE, Howder C, Berden G, Oomens J, Armentrout PB. Structural Elucidation of Biological and Toxicological Complexes: Investigation of Monomeric and Dimeric Complexes of Histidine with Multiply Charged Transition Metal (Zn and Cd) Cations using IR Action Spectroscopy. J Phys Chem B 2011; 115:12648-61. [DOI: 10.1021/jp207294b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Theresa E. Hofstetter
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah 84112, United States
| | - Collin Howder
- Department of Biology and Chemistry, Spring Arbor University, 106 E. Main St., Spring Arbor, Michigan 49283, United States
| | - Giel Berden
- FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, NL-3439 MN Nieuwegein, The Netherlands
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah 84112, United States
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Abstract
The development of facile forward and reverse genetic approaches has propelled the deconvolution of gene function in biology. While the origins of these techniques reside in the study of single-cell or invertebrate organisms, in many cases these approaches have been applied to vertebrate model systems to gain powerful insights into gene function during embryonic development. This perspective provides a summary of the major forward and reverse genetic approaches that have contributed to the study of vertebrate gene function in zebrafish, which has become an established model for the study of animal development.
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Affiliation(s)
- Nathan D Lawson
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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Nunez N, Clifton MMK, Funnell APW, Artuz C, Hallal S, Quinlan KGR, Font J, Vandevenne M, Setiyaputra S, Pearson RCM, Mackay JP, Crossley M. The multi-zinc finger protein ZNF217 contacts DNA through a two-finger domain. J Biol Chem 2011; 286:38190-38201. [PMID: 21908891 DOI: 10.1074/jbc.m111.301234] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Classical C2H2 zinc finger proteins are among the most abundant transcription factors found in eukaryotes, and the mechanisms through which they recognize their target genes have been extensively investigated. In general, a tandem array of three fingers separated by characteristic TGERP links is required for sequence-specific DNA recognition. Nevertheless, a significant number of zinc finger proteins do not contain a hallmark three-finger array of this type, raising the question of whether and how they contact DNA. We have examined the multi-finger protein ZNF217, which contains eight classical zinc fingers. ZNF217 is implicated as an oncogene and in repressing the E-cadherin gene. We show that two of its zinc fingers, 6 and 7, can mediate contacts with DNA. We examine its putative recognition site in the E-cadherin promoter and demonstrate that this is a suboptimal site. NMR analysis and mutagenesis is used to define the DNA binding surface of ZNF217, and we examine the specificity of the DNA binding activity using fluorescence anisotropy titrations. Finally, sequence analysis reveals that a variety of multi-finger proteins also contain two-finger units, and our data support the idea that these may constitute a distinct subclass of DNA recognition motif.
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Affiliation(s)
- Noelia Nunez
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Molly M K Clifton
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Alister P W Funnell
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales 2052, Australia
| | - Crisbel Artuz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales 2052, Australia
| | - Samantha Hallal
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Kate G R Quinlan
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Josep Font
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Marylène Vandevenne
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Surya Setiyaputra
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Richard C M Pearson
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales 2052, Australia
| | - Joel P Mackay
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia
| | - Merlin Crossley
- School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales 2052, Australia.
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50
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Lam KN, van Bakel H, Cote AG, van der Ven A, Hughes TR. Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays. Nucleic Acids Res 2011; 39:4680-90. [PMID: 21321018 PMCID: PMC3113560 DOI: 10.1093/nar/gkq1303] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [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: 08/04/2010] [Revised: 12/02/2010] [Accepted: 12/06/2010] [Indexed: 01/31/2023] Open
Abstract
C2H2 zinc fingers (C2H2-ZFs) are the most prevalent type of vertebrate DNA-binding domain, and typically appear in tandem arrays (ZFAs), with sequential C2H2-ZFs each contacting three (or more) sequential bases. C2H2-ZFs can be assembled in a modular fashion, providing one explanation for their remarkable evolutionary success. Given a set of modules with defined three-base specificities, modular assembly also presents a way to construct artificial proteins with specific DNA-binding preferences. However, a recent survey of a large number of three-finger ZFAs engineered by modular assembly reported high failure rates (∼70%), casting doubt on the generality of modular assembly. Here, we used protein-binding microarrays to analyze 28 ZFAs that failed in the aforementioned study. Most (17) preferred specific sequences, which in all but one case resembled the intended target sequence. Like natural ZFAs, the engineered ZFAs typically yielded degenerate motifs, binding dozens to hundreds of related individual sequences. Thus, the failure of these proteins in previous assays is not due to lack of sequence-specific DNA-binding activity. Our findings underscore the relevance of individual C2H2-ZF sequence specificities within tandem arrays, and support the general ability of modular assembly to produce ZFAs with sequence-specific DNA-binding activity.
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Affiliation(s)
- Kathy N. Lam
- Department of Molecular Genetics and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Harm van Bakel
- Department of Molecular Genetics and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Atina G. Cote
- Department of Molecular Genetics and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Anton van der Ven
- Department of Molecular Genetics and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Timothy R. Hughes
- Department of Molecular Genetics and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
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