1
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Fisher AJ, Beal PA. Structural perspectives on adenosine to inosine RNA editing by ADARs. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102284. [PMID: 39165563 PMCID: PMC11334849 DOI: 10.1016/j.omtn.2024.102284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Adenosine deaminases acting on RNA (ADARs) are enzymes that catalyze the hydrolytic deamination of adenosine to inosine. The editing feature of ADARs has garnered much attention as a therapeutic tool to repurpose ADARs to correct disease-causing mutations at the mRNA level in a technique called site-directed RNA editing (SDRE). Administering a short guide RNA oligonucleotide that hybridizes to a mutant sequence forms the requisite dsRNA substrate, directing ADARs to edit the desired adenosine. However, much is still unknown about ADARs' selectivity and sequence-specific effects on editing. Atomic-resolution structures can help provide additional insight to ADARs' selectivity and lead to novel guide RNA designs. Indeed, recent structures of ADAR domains have expanded our understanding on RNA binding and the base-flipping catalytic mechanism. These efforts have enabled the rational design of improved ADAR guide strands and advanced the therapeutic potential of the SDRE approach. While no full-length structure of any ADAR is known, this review presents an exposition of the structural basis for function of the different ADAR domains, focusing on human ADAR2. Key insights are extrapolated to human ADAR1, which is of substantial interest because of its widespread expression in most human tissues.
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Affiliation(s)
- Andrew J. Fisher
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
- Department of Molecular and Cellular Biology, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
| | - Peter A. Beal
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
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2
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Beck LG, Krall JB, Nichols PJ, Vicens Q, Henen MA, Vögeli B. Solution NMR backbone assignment of the N-terminal tandem Zα1-Zα2 domains of Z-DNA binding protein 1. BIOMOLECULAR NMR ASSIGNMENTS 2024:10.1007/s12104-024-10195-1. [PMID: 39215796 DOI: 10.1007/s12104-024-10195-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
The detection of nucleic acids that are present in atypical conformations is a crucial trigger of the innate immune response. Human Z-DNA binding protein 1 (ZBP1) is a pattern recognition receptor that harbors two Zα domains that recognize Z-DNA and Z-RNA. ZBP1 detects this alternate nucleic acid conformation as foreign, and upon stabilization of these substrates, it triggers activation of an immune response. Here, we present the backbone chemical shift assignment of a construct encompassing the Zα1 and Zα2 domains as well as the interconnecting linker of ZBP1. These assignments can be directly transferred to the isolated Zα1 and Zα2 domains, thereby demonstrating that these domains maintain virtually identical structures in the tandem context.
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Affiliation(s)
- Lily G Beck
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jeffrey B Krall
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Quentin Vicens
- Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX, 77204, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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3
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Langeberg CJ, Nichols PJ, Henen MA, Vicens Q, Vögeli B. Differential Structural Features of Two Mutant ADAR1p150 Zα Domains Associated with Aicardi-Goutières Syndrome. J Mol Biol 2023; 435:168040. [PMID: 36889460 PMCID: PMC10109538 DOI: 10.1016/j.jmb.2023.168040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023]
Abstract
The Zα domain of ADARp150 is critical for proper Z-RNA substrate binding and is a key factor in the type-I interferon response pathway. Two point-mutations in this domain (N173S and P193A), which cause neurodegenerative disorders, are linked to decreased A-to-I editing in disease models. To understand this phenomenon at the molecular level, we biophysically and structurally characterized these two mutated domains, revealing that they bind Z-RNA with a decreased affinity. Less efficient binding to Z-RNA can be explained by structural changes in beta-wing, part of the Z-RNA-protein interface, and alteration of conformational dynamics of the proteins.
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Affiliation(s)
- Conner J Langeberg
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
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4
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Abstract
The B-DNA to Z-DNA transition is a remarkable conformational change in DNA, which was originally observed in poly-GC DNA in the presence of high salt concentration. This eventually prompted the observation of the crystal structure of Z-DNA, a left-handed double-helical DNA, at atomic resolution. Despite advances in Z-DNA research, the application of circular dichroism (CD) spectroscopy as the fundamental technique to characterize this unique DNA conformation has remained constant. In this chapter, we describe a CD spectroscopic method for characterizing the B-DNA to Z-DNA transition of a CG-repeat double-stranded DNA fragment formed from a protein or chemical inducer.
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Affiliation(s)
- Vinod Kumar Subramani
- Department of Precision Medicine, Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, South Korea.
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, South Korea
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5
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Characterization of Z-DNA by Infrared Spectroscopy. Methods Mol Biol 2023; 2651:53-58. [PMID: 36892758 DOI: 10.1007/978-1-0716-3084-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Infrared spectrum stems from the matter's absorption of light in the infrared (IR) light region. Generally, this infrared light absorption is due to the transition of vibrational and rotational energy levels of the involved molecule. Since different molecules have different structures and vibration modes, infrared spectroscopy can therefore be widely applied to analyze the chemical compositions and structures of molecules. Here we describe the method of application of infrared spectroscopy in the investigation of Z-DNA in cells, as infrared spectroscopy can distinguish DNA secondary structures sensitively and the band at 930 cm-1 is specifically attributed to the Z-form DNA. Based on the curve fitting, the relative content of Z-DNA in the cells may be evaluated.
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6
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Diallo MA, Pirotte S, Hu Y, Morvan L, Rakus K, Suárez NM, PoTsang L, Saneyoshi H, Xu Y, Davison A, Tompa P, Sussman J, Vanderplasschen A. A fish herpesvirus highlights functional diversities among Zα domains related to phase separation induction and A-to-Z conversion. Nucleic Acids Res 2022; 51:806-830. [PMID: 36130731 PMCID: PMC9881149 DOI: 10.1093/nar/gkac761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 02/06/2023] Open
Abstract
Zalpha (Zα) domains bind to left-handed Z-DNA and Z-RNA. The Zα domain protein family includes cellular (ADAR1, ZBP1 and PKZ) and viral (vaccinia virus E3 and cyprinid herpesvirus 3 (CyHV-3) ORF112) proteins. We studied CyHV-3 ORF112, which contains an intrinsically disordered region and a Zα domain. Genome editing of CyHV-3 indicated that the expression of only the Zα domain of ORF112 was sufficient for normal viral replication in cell culture and virulence in carp. In contrast, its deletion was lethal for the virus. These observations revealed the potential of the CyHV-3 model as a unique platform to compare the exchangeability of Zα domains expressed alone in living cells. Attempts to rescue the ORF112 deletion by a broad spectrum of cellular, viral, and artificial Zα domains showed that only those expressing Z-binding activity, the capacity to induce liquid-liquid phase separation (LLPS), and A-to-Z conversion, could rescue viral replication. For the first time, this study reports the ability of some Zα domains to induce LLPS and supports the biological relevance of dsRNA A-to-Z conversion mediated by Zα domains. This study expands the functional diversity of Zα domains and stimulates new hypotheses concerning the mechanisms of action of proteins containing Zα domains.
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Affiliation(s)
| | | | - Yunlong Hu
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium
| | - Léa Morvan
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium
| | - Krzysztof Rakus
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium,Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow 30387, Poland
| | - Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Lee PoTsang
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium,Department of Aquaculture, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Hisao Saneyoshi
- Department of Medical Sciences, Division of Chemistry, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yan Xu
- Department of Medical Sciences, Division of Chemistry, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussel B-1050, Belgium
| | - Joel L Sussman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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7
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Meng Y, Wang G, He H, Lau KH, Hurt A, Bixler BJ, Parham A, Jin SG, Xu X, Vasquez KM, Pfeifer GP, Szabó PE. Z-DNA is remodelled by ZBTB43 in prospermatogonia to safeguard the germline genome and epigenome. Nat Cell Biol 2022; 24:1141-1153. [PMID: 35787683 PMCID: PMC9276527 DOI: 10.1038/s41556-022-00941-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 05/17/2022] [Indexed: 12/12/2022]
Abstract
Mutagenic purine–pyrimidine repeats can adopt the left-handed Z-DNA conformation. DNA breaks at potential Z-DNA sites can lead to somatic mutations in cancer or to germline mutations that are transmitted to the next generation. It is not known whether any mechanism exists in the germ line to control Z-DNA structure and DNA breaks at purine–pyrimidine repeats. Here we provide genetic, epigenomic and biochemical evidence for the existence of a biological process that erases Z-DNA specifically in germ cells of the mouse male foetus. We show that a previously uncharacterized zinc finger protein, ZBTB43, binds to and removes Z-DNA, preventing the formation of DNA double-strand breaks. By removing Z-DNA, ZBTB43 also promotes de novo DNA methylation at CG-containing purine–pyrimidine repeats in prospermatogonia. Therefore, the genomic and epigenomic integrity of the species is safeguarded by remodelling DNA structure in the mammalian germ line during a critical window of germline epigenome reprogramming. Meng et al. show that ZBTB43 alters Z-DNA structures to prevent deleterious double-strand breaks and promote DNA methylation at purine–pyrimidine repeats in the mouse germ line.
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Affiliation(s)
- Yingying Meng
- Capital Normal University College of Life Science, Beijing, China.,Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Hongjuan He
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.,School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Kin H Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Allison Hurt
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Brianna J Bixler
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Andrea Parham
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.,Van Andel Institute Graduate School, Grand Rapids, MI, USA
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Xingzhi Xu
- Capital Normal University College of Life Science, Beijing, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Piroska E Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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8
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Szczerba M, Subramanian S, Trainor K, McCaughan M, Kibler KV, Jacobs BL. Small Hero with Great Powers: Vaccinia Virus E3 Protein and Evasion of the Type I IFN Response. Biomedicines 2022; 10:biomedicines10020235. [PMID: 35203445 PMCID: PMC8869630 DOI: 10.3390/biomedicines10020235] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 12/14/2022] Open
Abstract
Poxviridae have developed a plethora of strategies to evade innate and adaptive immunity. In this review, we focused on the vaccinia virus E3 protein, encoded by the E3L gene. E3 is present within the Chordopoxvirinae subfamily (with the exception of the avipoxviruses and molluscum contagiosum virus) and displays pleiotropic effects on the innate immune system. Initial studies identified E3 as a double-stranded RNA (dsRNA)-binding protein (through its C terminus), able to inhibit the activation of protein kinase dependent on RNA (PKR) and the 2′5′-oligoadenylate synthetase (OAS)/RNase L pathway, rendering E3 a protein counteracting the type I interferon (IFN) system. In recent years, N-terminal mutants of E3 unable to bind to Z-form nucleic acids have been shown to induce the cellular death pathway necroptosis. This pathway was dependent on host IFN-inducible Z-DNA-binding protein 1 (ZBP1); full-length E3 is able to inhibit ZBP1-mediated necroptosis. Binding to what was identified as Z-RNA has emerged as a novel mechanism of counteracting the type I IFN system and has broadened our understanding of innate immunity against viral infections. This article gives an overview of the studies leading to our understanding of the vaccinia virus E3 protein function and its involvement in viral pathogenesis. Furthermore, a short summary of other viral systems is provided.
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Affiliation(s)
- Mateusz Szczerba
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85281, USA; (M.S.); (S.S.); (K.T.); (M.M.); (K.V.K.)
| | - Sambhavi Subramanian
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85281, USA; (M.S.); (S.S.); (K.T.); (M.M.); (K.V.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Kelly Trainor
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85281, USA; (M.S.); (S.S.); (K.T.); (M.M.); (K.V.K.)
- Faculty of Biology, Coconino Community College, Flagstaff, AZ 86005, USA
| | - Megan McCaughan
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85281, USA; (M.S.); (S.S.); (K.T.); (M.M.); (K.V.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Karen V. Kibler
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85281, USA; (M.S.); (S.S.); (K.T.); (M.M.); (K.V.K.)
| | - Bertram L. Jacobs
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85281, USA; (M.S.); (S.S.); (K.T.); (M.M.); (K.V.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Correspondence:
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9
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Nichols PJ, Henen MA, Vicens Q, Vögeli B. Solution NMR backbone assignments of the N-terminal Zα-linker-Zβ segment from Homo sapiens ADAR1p150. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:273-279. [PMID: 33742389 PMCID: PMC9199369 DOI: 10.1007/s12104-021-10017-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Adenosine-to-inosine (A-to-I) editing of a subset of RNAs in a eukaryotic cell is required in order to avoid triggering the innate immune system. Editing is carried out by ADAR1, which exists as short (p110) and long (p150) isoforms. ADAR1p150 is mostly cytoplasmic, possesses a Z-RNA binding domain (Zα), and is only expressed during the innate immune response. A structurally homologous domain to Zα, the Zβ domain, is separated by a long linker from Zα on the N-terminus of ADAR1 but its function remains unknown. Zβ does not bind to RNA in isolation, yet the binding kinetics of the segment encompassing Zα, Zβ and the 95-residue linker between the two domains (Zα-Zβ) are markedly different compared to Zα alone. Here we present the solution NMR backbone assignment of Zα-Zβ from H. Sapiens ADAR1. The predicted secondary structure of Zα-Zβ based on chemical shifts is in agreement with previously determined structures of Zα and Zβ in isolation, and indicates that the linker is intrinsically disordered. Comparison of the chemical shifts between the individual Zα and Zβ domains to the full Zα-Zβ construct suggests that Zβ may interact with the linker, the function of which is currently unknown.
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Affiliation(s)
- Parker J Nichols
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Morkos A Henen
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Quentin Vicens
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA.
| | - Beat Vögeli
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Colorado, 12801 E. 17th Avenue, Aurora, CO, 80045, USA.
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10
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Kim SH, Jung HJ, Lee IB, Lee NK, Hong SC. Sequence-dependent cost for Z-form shapes the torsion-driven B-Z transition via close interplay of Z-DNA and DNA bubble. Nucleic Acids Res 2021; 49:3651-3660. [PMID: 33744929 PMCID: PMC8053131 DOI: 10.1093/nar/gkab153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 02/19/2021] [Accepted: 02/27/2021] [Indexed: 02/06/2023] Open
Abstract
Despite recent genome-wide investigations of functional DNA elements, the mechanistic details about their actions remain elusive. One intriguing possibility is that DNA sequences with special patterns play biological roles, adopting non-B-DNA conformations. Here we investigated dynamics of thymine-guanine (TG) repeats, microsatellite sequences and recurrently found in promoters, as well as cytosine–guanine (CG) repeats, best-known Z-DNA forming sequence, in the aspect of Z-DNA formation. We measured the energy barriers of the B–Z transition with those repeats and discovered the sequence-dependent penalty for Z-DNA generates distinctive thermodynamic and kinetic features in the torque-induced transition. Due to the higher torsional stress required for Z-form in TG repeats, a bubble could be induced more easily, suppressing Z-DNA induction, but facilitate the B–Z interconversion kinetically at the transition midpoint. Thus, the Z-form by TG repeats has advantages as a torsion buffer and bubble selector while the Z-form by CG repeats likely behaves as torsion absorber. Our statistical physics model supports quantitatively the populations of Z-DNA and reveals the pivotal roles of bubbles in state dynamics. All taken together, a quantitative picture for the transition was deduced within the close interplay among bubbles, plectonemes and Z-DNA.
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Affiliation(s)
- Sook Ho Kim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841 Korea.,Department of Physics, Korea University, Seoul, 02841 Korea.,GRI-TPC International Research Center, Sejong University, Seoul, 05006 Korea
| | - Hae Jun Jung
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841 Korea.,Department of Physics, Korea University, Seoul, 02841 Korea
| | - Il-Buem Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841 Korea.,Department of Physics, Korea University, Seoul, 02841 Korea
| | - Nam-Kyung Lee
- Department of Physics and Astronomy, Sejong University, Seoul, 05006 Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841 Korea.,Department of Physics, Korea University, Seoul, 02841 Korea
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11
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Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions. Nat Commun 2021; 12:793. [PMID: 33542240 PMCID: PMC7862695 DOI: 10.1038/s41467-021-21039-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/07/2021] [Indexed: 12/11/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) editing of eukaryotic cellular RNAs is essential for protection against auto-immune disorders. Editing is carried out by ADAR1, whose innate immune response-specific cytoplasmic isoform possesses a Z-DNA binding domain (Zα) of unknown function. Zα also binds to CpG repeats in RNA, which are a hallmark of Z-RNA formation. Unexpectedly, Zα has been predicted — and in some cases even shown — to bind to specific regions within mRNA and rRNA devoid of such repeats. Here, we use NMR, circular dichroism, and other biophysical approaches to demonstrate and characterize the binding of Zα to mRNA and rRNA fragments. Our results reveal a broad range of RNA sequences that bind to Zα and adopt Z-RNA conformations. Binding is accompanied by destabilization of neighboring A-form regions which is similar in character to what has been observed for B-Z-DNA junctions. The binding of Zα to non-CpG sequences is specific, cooperative and occurs with an affinity in the low micromolar range. This work allows us to propose a model for how Zα could influence the RNA binding specificity of ADAR1. ADAR1 is an interferon-induced enzyme that catalyzes editing of adenine to inosine across the transcriptome as part of the immune response. Here the authors establish how ADAR1 recognizes non-CpG RNA sequences to facilitate the formation of A-Z junctions.
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12
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Abstract
The innate immune receptors in higher organisms have evolved to detect molecular signatures associated with pathogenic infection and trigger appropriate immune response. One common class of molecules utilized by the innate immune system for self vs. nonself discrimination is RNA, which is ironically present in all forms of life. To avoid self-RNA recognition, the innate immune sensors have evolved sophisticated discriminatory mechanisms that involve cellular RNA metabolic machineries. Posttranscriptional RNA modification and editing represent one such mechanism that allows cells to chemically tag the host RNAs as "self" and thus tolerate the abundant self-RNA molecules. In this chapter, we discuss recent advances in our understanding of the role of RNA editing/modification in the modulation of immune signaling pathways, and application of RNA editing/modification in RNA-based therapeutics and cancer immunotherapies.
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13
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Shin SI, Ham S, Park J, Seo SH, Lim CH, Jeon H, Huh J, Roh TY. Z-DNA-forming sites identified by ChIP-Seq are associated with actively transcribed regions in the human genome. DNA Res 2016; 23:477-486. [PMID: 27374614 PMCID: PMC5066173 DOI: 10.1093/dnares/dsw031] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 06/03/2016] [Indexed: 01/08/2023] Open
Abstract
Z-DNA, a left-handed double helical DNA is structurally different from the most abundant B-DNA. Z-DNA has been known to play a significant role in transcription and genome stability but the biological meaning and positions of Z-DNA-forming sites (ZFSs) in the human genome has not been fully explored. To obtain genome-wide map of ZFSs, Zaa with two Z-DNA-binding domains was used for ChIP-Seq analysis. A total of 391 ZFSs were found and their functions were examined in vivo. A large portion of ZFSs was enriched in the promoter regions and contain sequences with high potential to form Z-DNA. Genes containing ZFSs were occupied by RNA polymerase II at the promoters and showed high levels of expression. Moreover, ZFSs were significantly related to active histone marks such as H3K4me3 and H3K9ac. The association of Z-DNA with active transcription was confirmed by the reporter assay system. Overall, our results suggest that Z-DNA formation depends on chromatin structure as well as sequence composition, and is associated with active transcription in human cells. The global information about ZFSs positioning will provide a useful resource for further understanding of DNA structure-dependent transcriptional regulation.
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Affiliation(s)
| | | | - Jihwan Park
- Division of Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | | | - Chae Hyun Lim
- Division of Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | | | | | - Tae-Young Roh
- Department of Life Sciences.,Division of Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
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14
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Man SM, Karki R, Kanneganti TD. DNA-sensing inflammasomes: regulation of bacterial host defense and the gut microbiota. Pathog Dis 2016; 74:ftw028. [PMID: 27056948 DOI: 10.1093/femspd/ftw028] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2016] [Indexed: 02/07/2023] Open
Abstract
DNA sensors are formidable immune guardians of the host. At least 14 cytoplasmic DNA sensors have been identified in recent years, each with specialized roles in driving inflammation and/or cell death. Of these, AIM2 is a sensor of dsDNA, and forms an inflammasome complex to activate the cysteine protease caspase-1, mediates the release of the proinflammatory cytokines IL-1β and IL-18, and induces pyroptosis. The inflammasome sensor NLRP3 can also respond to DNA in the forms of oxidized mitochondrial DNA and the DNA derivative RNA:DNA hybrids produced by bacteria, whereas the putative inflammasome sensor IFI16 responds to viral DNA in the nucleus. Although inflammasomes provoke inflammation for anti-microbial host defense, they must also maintain homeostasis with commensal microbiota. Here, we outline recent advances highlighting the complex relationship between DNA-sensing inflammasomes, bacterial host defense and the gut microbiota.
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Affiliation(s)
- Si Ming Man
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Rajendra Karki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
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15
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Mannion N, Arieti F, Gallo A, Keegan LP, O'Connell MA. New Insights into the Biological Role of Mammalian ADARs; the RNA Editing Proteins. Biomolecules 2015; 5:2338-62. [PMID: 26437436 PMCID: PMC4693238 DOI: 10.3390/biom5042338] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/09/2015] [Accepted: 09/11/2015] [Indexed: 12/20/2022] Open
Abstract
The ADAR proteins deaminate adenosine to inosine in double-stranded RNA which is one of the most abundant modifications present in mammalian RNA. Inosine can have a profound effect on the RNAs that are edited, not only changing the base-pairing properties, but can also result in recoding, as inosine behaves as if it were guanosine. In mammals there are three ADAR proteins and two ADAR-related proteins (ADAD) expressed. All have a very similar modular structure; however, both their expression and biological function differ significantly. Only two of the ADAR proteins have enzymatic activity. However, both ADAR and ADAD proteins possess the ability to bind double-strand RNA. Mutations in ADARs have been associated with many diseases ranging from cancer, innate immunity to neurological disorders. Here, we will discuss in detail the domain structure of mammalian ADARs, the effects of RNA editing, and the role of ADARs in human diseases.
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Affiliation(s)
- Niamh Mannion
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, 21 Shelley Road, Glasgow G12 0ZD, UK.
| | - Fabiana Arieti
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.
| | - Angela Gallo
- Oncohaematoogy Department, Ospedale Pediatrico Bambino Gesù (IRCCS) Viale di San Paolo, Roma 15-00146, Italy.
| | - Liam P Keegan
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.
| | - Mary A O'Connell
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.
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16
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Vlijm R, Mashaghi A, Bernard S, Modesti M, Dekker C. Experimental phase diagram of negatively supercoiled DNA measured by magnetic tweezers and fluorescence. NANOSCALE 2015; 7:3205-3216. [PMID: 25615283 DOI: 10.1039/c4nr04332d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The most common form of DNA is the well-known B-structure of double-helix DNA. Many processes in the cell, however, exert force and torque, inducing structural changes to the DNA that are vital to biological function. Virtually all DNA in cells is in a state of negative supercoiling, with a DNA structure that is complex. Using magnetic tweezers combined with fluorescence imaging, we here study DNA structure as a function of negative supercoiling at the single-molecule level. We classify DNA phases based on DNA length as a function of supercoiling, down to a very high negative supercoiling density σ of -2.5, and forces up to 4.5 pN. We characterize plectonemes using fluorescence imaging. DNA bubbles are visualized by the binding of fluorescently labelled RPA, a eukaryotic single-strand-binding protein. The presence of Z-DNA, a left-handed form of DNA, is probed by the binding of Zα77, the minimal binding domain of a Z-DNA-binding protein. Without supercoiling, DNA is in the relaxed B-form. Upon going toward negative supercoiling, plectonemic B-DNA is being formed below 0.6 pN. At higher forces and supercoiling densities down to about -1.9, a mixed state occurs with plectonemes, multiple bubbles and left-handed L-DNA. Around σ = -1.9, a buckling transition occurs after which the DNA end-to-end length linearly decreases when applying more negative turns, into a state that we interpret as plectonemic L-DNA. By measuring DNA length, Zα77 binding, plectoneme and ssDNA visualisation, we thus have mapped the co-existence of many DNA structures and experimentally determined the DNA phase diagram at (extreme) negative supercoiling.
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Affiliation(s)
- Rifka Vlijm
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands.
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17
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de Rosa M, Zacarias S, Athanasiadis A. Structural basis for Z-DNA binding and stabilization by the zebrafish Z-DNA dependent protein kinase PKZ. Nucleic Acids Res 2013; 41:9924-33. [PMID: 23975196 PMCID: PMC3834819 DOI: 10.1093/nar/gkt743] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The RNA-dependent protein kinase PKR plays a central role in the antiviral defense of vertebrates by shutting down protein translation upon detection of viral dsRNA in the cytoplasm. In some teleost fish, PKZ, a homolog of PKR, performs the same function, but surprisingly, instead of dsRNA binding domains, it harbors two Z-DNA/Z-RNA-binding domains belonging to the Zalpha domain family. Zalpha domains have also been found in other proteins, which have key roles in the regulation of interferon responses such as ADAR1 and DNA-dependent activator of IFN-regulatory factors (DAI) and in viral proteins involved in immune response evasion such as the poxviral E3L and the Cyprinid Herpesvirus 3 ORF112. The underlying mechanism of nucleic acids binding and stabilization by Zalpha domains is still unclear. Here, we present two crystal structures of the zebrafish PKZ Zalpha domain (DrZalphaPKZ) in alternatively organized complexes with a (CG)6 DNA oligonucleotide at 2 and 1.8 Å resolution. These structures reveal novel aspects of the Zalpha interaction with DNA, and they give insights on the arrangement of multiple Zalpha domains on DNA helices longer than the minimal binding site.
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Affiliation(s)
| | | | - Alekos Athanasiadis
- *To whom correspondence should be addressed. Tel: +351 21 4464648; Fax: +351 21 4407970;
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18
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Bothe JR, Lowenhaupt K, Al-Hashimi HM. Incorporation of CC steps into Z-DNA: interplay between B-Z junction and Z-DNA helical formation. Biochemistry 2012; 51:6871-9. [PMID: 22873788 DOI: 10.1021/bi300785b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The left-handed DNA structure, Z-DNA, is believed to play important roles in gene expression and regulation. Z-DNA forms sequence-specifically with a preference for sequences rich in pyrimidine/purine dinucleotide steps. In vivo, Z-DNA is generated in the presence of negative supercoiling or upon binding proteins that absorb the high energetic cost of the B-to-Z transition, including the creation of distorted junctions between B-DNA and Z-DNA. To date, the sequence preferences for the B-to-Z transition have primarily been studied in the context of sequence repeats lacking B-Z junctions. Here, we develop a method for characterizing sequence-specific preferences for Z-DNA formation and B-Z junction localization within heterogeneous DNA duplexes that is based on combining 2-aminopurine fluorescence measurements with a new quantitative application of circular dichroism spectroscopy for determining the fraction of B- versus Z-DNA. Using this approach, we show that at least three consecutive CC dinucleotide steps, traditionally thought to disfavor Z-DNA, can be incorporated within heterogeneous Z-DNA containing B-Z junctions upon binding to the Zα domain of the RNA adenosine deaminase protein. Our results indicate that the incorporation of CC steps into Z-DNA is driven by favorable sequence-specific Z-Z and B-Z stacking interactions as well as by sequence-specific energetics that localize the distorted B-Z junction at flexible sites. Together, our results expose higher-order complexities in the Z-DNA code within heterogeneous sequences and suggest that Z-DNA can in principle propagate into a wider range of genomic sequence elements than previously thought.
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Affiliation(s)
- Jameson R Bothe
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
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Klocko AD, Schroeder JW, Walsh BW, Lenhart JS, Evans ML, Simmons LA. Mismatch repair causes the dynamic release of an essential DNA polymerase from the replication fork. Mol Microbiol 2011; 82:648-63. [PMID: 21958350 DOI: 10.1111/j.1365-2958.2011.07841.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mismatch repair (MMR) corrects DNA polymerase errors occurring during genome replication. MMR is critical for genome maintenance, and its loss increases mutation rates several hundred fold. Recent work has shown that the interaction between the mismatch recognition protein MutS and the replication processivity clamp is important for MMR in Bacillus subtilis. To further understand how MMR is coupled to DNA replication, we examined the subcellular localization of MMR and DNA replication proteins fused to green fluorescent protein (GFP) in live cells, following an increase in DNA replication errors. We demonstrate that foci of the essential DNA polymerase DnaE-GFP decrease following mismatch incorporation and that loss of DnaE-GFP foci requires MutS. Furthermore, we show that MutS and MutL bind DnaE in vitro, suggesting that DnaE is coupled to repair. We also found that DnaE-GFP foci decrease in vivo following a DNA damage-independent arrest of DNA synthesis showing that loss of DnaE-GFP foci is caused by perturbations to DNA replication. We propose that MutS directly contacts the DNA replication machinery, causing a dynamic change in the organization of DnaE at the replication fork during MMR. Our results establish a striking and intimate connection between MMR and the replicating DNA polymerase complex in vivo.
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Affiliation(s)
- Andrew D Klocko
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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20
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Kim YG, Chi JS, Lee SM, Kwon NS, Baek KJ, Yun HY. Efficient Ribosomal Frameshifitng Can Occur at the Beginning of the Translation. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.9.3489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Barraud P, Allain FHT. ADAR proteins: double-stranded RNA and Z-DNA binding domains. Curr Top Microbiol Immunol 2011; 353:35-60. [PMID: 21728134 DOI: 10.1007/82_2011_145] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Adenosine deaminases acting on RNA (ADAR) catalyze adenosine to inosine editing within double-stranded RNA (dsRNA) substrates. Inosine is read as a guanine by most cellular processes and therefore these changes create codons for a different amino acid, stop codons or even a new splice-site allowing protein diversity generated from a single gene. We review here the current structural and molecular knowledge on RNA editing by the ADAR family of protein. We focus especially on two types of nucleic acid binding domains present in ADARs, namely the dsRNA and Z-DNA binding domains.
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Affiliation(s)
- Pierre Barraud
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zürich, Switzerland
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22
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Ha SC, Choi J, Hwang HY, Rich A, Kim YG, Kim KK. The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ alpha(ADAR1). Nucleic Acids Res 2008; 37:629-37. [PMID: 19074195 PMCID: PMC2632926 DOI: 10.1093/nar/gkn976] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Z-DNA conformation preferentially occurs at alternating purine-pyrimidine repeats, and is specifically recognized by Z alpha domains identified in several Z-DNA-binding proteins. The binding of Z alpha to foreign or chromosomal DNA in various sequence contexts is known to influence various biological functions, including the DNA-mediated innate immune response and transcriptional modulation of gene expression. For these reasons, understanding its binding mode and the conformational diversity of Z alpha bound Z-DNAs is of considerable importance. However, structural studies of Z alpha bound Z-DNA have been mostly limited to standard CG-repeat DNAs. Here, we have solved the crystal structures of three representative non-CG repeat DNAs, d(CACGTG)(2), d(CGTACG)(2) and d(CGGCCG)(2) complexed to hZ alpha(ADAR1) and compared those structures with that of hZ alpha(ADAR1)/d(CGCGCG)(2) and the Z alpha-free Z-DNAs. hZ alpha(ADAR1) bound to each of the three Z-DNAs showed a well conserved binding mode with very limited structural deviation irrespective of the DNA sequence, although varying numbers of residues were in contact with Z-DNA. Z-DNAs display less structural alterations in the Z alpha-bound state than in their free form, thereby suggesting that conformational diversities of Z-DNAs are restrained by the binding pocket of Z alpha. These data suggest that Z-DNAs are recognized by Z alpha through common conformational features regardless of the sequence and structural alterations.
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Affiliation(s)
- Sung Chul Ha
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
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Lippmann J, Rothenburg S, Deigendesch N, Eitel J, Meixenberger K, van Laak V, Slevogt H, N'guessan PD, Hippenstiel S, Chakraborty T, Flieger A, Suttorp N, Opitz B. IFNbeta responses induced by intracellular bacteria or cytosolic DNA in different human cells do not require ZBP1 (DLM-1/DAI). Cell Microbiol 2008; 10:2579-88. [PMID: 18771559 DOI: 10.1111/j.1462-5822.2008.01232.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intracellular bacteria and cytosolic stimulation with DNA activate type I IFN responses independently of Toll-like receptors, most Nod-like receptors and RIG-like receptors. A recent study suggested that ZBP1 (DLM-1/DAI) represents the long anticipated pattern recognition receptor which mediates IFNalpha/beta responses to cytosolic DNA in mice. Here we show that Legionella pneumophila infection, and intracellular challenge with poly(dA-dT), but not with poly(dG-dC), induced expression of IFNbeta, full-length hZBP1 and a prominent splice variant lacking the first Zalpha domain (hZBP1DeltaZalpha) in human cells. Overexpression of hZBP1 but not hZBP1DeltaZalpha slightly amplified poly(dA-dT)-stimulated IFNbeta reporter activation in HEK293 cells, but had no effect on IFNbeta and IL-8 production induced by bacteria or poly(dA-dT) in A549 cells. We found that mZBP1 siRNA impaired poly(dA-dT)-induced IFNbeta responses in mouse L929 fibroblasts at a later time point, while multiple hZBP1 siRNAs did not suppress IFNbeta or IL-8 expression induced by poly(dA-dT) or bacterial infection in human cells. In contrast, IRF3 siRNA strongly impaired the IFNbeta responses to poly(dA-dT) or bacterial infection. In conclusion, intracellular bacteria and cytosolic poly(dA-dT) activate IFNbeta responses in different human cells without requiring human ZBP1.
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Affiliation(s)
- Juliane Lippmann
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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24
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Rothenburg S, Deigendesch N, Dey M, Dever TE, Tazi L. Double-stranded RNA-activated protein kinase PKR of fishes and amphibians: varying the number of double-stranded RNA binding domains and lineage-specific duplications. BMC Biol 2008; 6:12. [PMID: 18312693 PMCID: PMC2291453 DOI: 10.1186/1741-7007-6-12] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 03/03/2008] [Indexed: 02/04/2023] Open
Abstract
Background Double-stranded (ds) RNA, generated during viral infection, binds and activates the mammalian anti-viral protein kinase PKR, which phosphorylates the translation initiation factor eIF2α leading to the general inhibition of protein synthesis. Although PKR-like activity has been described in fish cells, the responsible enzymes eluded molecular characterization until the recent discovery of goldfish and zebrafish PKZ, which contain Z-DNA-binding domains instead of dsRNA-binding domains (dsRBDs). Fish and amphibian PKR genes have not been described so far. Results Here we report the cloning and identification of 13 PKR genes from 8 teleost fish and amphibian species, including zebrafish, demonstrating the coexistence of PKR and PKZ in this latter species. Analyses of their genomic organization revealed up to three tandemly arrayed PKR genes, which are arranged in head-to-tail orientation. At least five duplications occurred independently in fish and amphibian lineages. Phylogenetic analyses reveal that the kinase domains of fish PKR genes are more closely related to those of fish PKZ than to the PKR kinase domains of other vertebrate species. The duplication leading to fish PKR and PKZ genes occurred early during teleost fish evolution after the divergence of the tetrapod lineage. While two dsRBDs are found in mammalian and amphibian PKR, one, two or three dsRBDs are present in fish PKR. In zebrafish, both PKR and PKZ were strongly upregulated after immunostimulation with some tissue-specific expression differences. Using genetic and biochemical assays we demonstrate that both zebrafish PKR and PKZ can phosphorylate eIF2α in yeast. Conclusion Considering the important role for PKR in host defense against viruses, the independent duplication and fixation of PKR genes in different lineages probably provided selective advantages by leading to the recognition of an extended spectrum of viral nucleic acid structures, including both dsRNA and Z-DNA/RNA, and perhaps by altering sensitivity to viral PKR inhibitors. Further implications of our findings for the evolution of the PKR family and for studying PKR/PKZ interactions with viral gene products and their roles in viral infections are discussed.
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Affiliation(s)
- Stefan Rothenburg
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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Binding Surface in Zβ Domain from Human ZBP1 Does Not Require Conserved Proline Residues for Z-DNA Binding and B-to-Z-DNA Conversion Activities. B KOREAN CHEM SOC 2007. [DOI: 10.5012/bkcs.2007.28.12.2539] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Quyen DV, Ha SC, Lowenhaupt K, Rich A, Kim KK, Kim YG. Characterization of DNA-binding activity of Z alpha domains from poxviruses and the importance of the beta-wing regions in converting B-DNA to Z-DNA. Nucleic Acids Res 2007; 35:7714-20. [PMID: 17984076 PMCID: PMC2190711 DOI: 10.1093/nar/gkm748] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The E3L gene is essential for pathogenesis in vaccinia virus. The E3L gene product consists of an N-terminal Zα domain and a C-terminal double-stranded RNA (dsRNA) binding domain; the left-handed Z-DNA-binding activity of the Zα domain of E3L is required for viral pathogenicity in mice. E3L is highly conserved among poxviruses, including the smallpox virus, and it is likely that the orthologous Zα domains play similar roles. To better understand the biological function of E3L proteins, we have investigated the Z-DNA-binding behavior of five representative Zα domains from poxviruses. Using surface plasmon resonance (SPR), we have demonstrated that these viral Zα domains bind Z-DNA tightly. Ability of ZαE3L converting B-DNA to Z-DNA was measured by circular dichroism (CD). The extents to which these Zαs can stabilize Z-DNA vary considerably. Mutational studies demonstrate that residues in the loop of the β-wing play an important role in this stabilization. Notably the Zα domain of vaccinia E3L acquires ability to convert B-DNA to Z-DNA by mutating amino acid residues in this region. Differences in the host cells of the various poxviruses may require different abilities to stabilize Z-DNA; this may be reflected in the observed differences in behavior in these Zα proteins.
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Affiliation(s)
- Dong Van Quyen
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
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Deigendesch N, Koch-Nolte F, Rothenburg S. ZBP1 subcellular localization and association with stress granules is controlled by its Z-DNA binding domains. Nucleic Acids Res 2006; 34:5007-20. [PMID: 16990255 PMCID: PMC1636418 DOI: 10.1093/nar/gkl575] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Z-DNA binding protein 1 (ZBP1) belongs to a family of proteins that contain the Zα domain, which binds specifically to left-handed Z-DNA and Z-RNA. Like all vertebrate proteins in the Zα family, it contains two Zα-like domains and is highly inducible by immunostimulation. Using circular dichroism spectroscopy and electrophoretic mobility shift assays we show that both Zα domains can bind Z-DNA independently and that substrate binding is greatly enhanced when both domains are linked. Full length ZBP1 and a prominent splice variant lacking the first Zα domain (ΔZα) showed strikingly different subcellular localizations. While the full length protein showed a finely punctate cytoplasmatic distribution, ZBP1ΔZα accumulated in large cytoplasmic granules. Mutation of residues important for Z-DNA binding in the first Zα domain resulted in a distribution comparable to that of ZBP1ΔZα. The ZBP1ΔZα granules are distinct from stress granules (SGs) and processing bodies but dynamically interacted with these. Polysome stabilization led to the disassembly of ZBP1ΔZα granules, indicating that mRNA are integral components. Heat shock and arsenite exposure had opposing effects on ZBP1 isoforms: while ZBP1ΔZα granules disassembled, full length ZBP1 accumulated in SGs. Our data link ZBP1 to mRNA sorting and metabolism and indicate distinct roles for ZBP1 isoforms.
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Affiliation(s)
- Nikolaus Deigendesch
- Institute for Immunology, University Hospital EppendorfHamburg, Germany
- Department of Biology, Massachusetts Institute of TechnologyCambridge, MA, USA
| | | | - Stefan Rothenburg
- Institute for Immunology, University Hospital EppendorfHamburg, Germany
- To whom correspondence should be addressed. Tel: +49 40 428037922; Fax: +49 40 428034243;
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Kim YG, Park HJ, Kim KK, Lowenhaupt K, Rich A. A peptide with alternating lysines can act as a highly specific Z-DNA binding domain. Nucleic Acids Res 2006; 34:4937-42. [PMID: 16982643 PMCID: PMC1635270 DOI: 10.1093/nar/gkl607] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many nucleic acid binding proteins use short peptide sequences to provide specificity in recognizing their targets, which may be either a specific sequence or a conformation. Peptides containing alternating lysine have been shown to bind to poly(dG–d5meC) in the Z conformation, and stabilize the higher energy form [H. Takeuchi, N. Hanamura, H. Hayasaka and I. Harada (1991) FEBS Lett., 279, 253–255 and H. Takeuchi, N. Hanamura and I. Harada (1994) J. Mol. Biol., 236, 610–617.]. Here we report the construction of a Z-DNA specific binding protein, with the peptide KGKGKGK as a functional domain and a leucine zipper as a dimerization domain. The resultant protein, KGZIP, induces the Z conformation in poly(dG–d5meC) and binds to Z-DNA stabilized by bromination with high affinity and specificity. The binding of KGZIP is sufficient to convert poly(dG–d5meC) from the B to the Z form, as shown by circular dichroism. The sequence KGKGKGK is found in many proteins, although no functional role has been established. KGZIP also has potential for engineering other Z-DNA specific proteins for future studies of Z-DNA in vitro and in vivo.
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Affiliation(s)
- Yang-Gyun Kim
- Department of Chemistry, Sungkyunkwan University300 Chunchundong, Jangangu, Suwon, Kyunggido 440-746, Korea
| | - Hyun-Ju Park
- College of Pharmacy, Sungkyunkwan University300 Chunchundong, Jangangu, Suwon, Kyunggido 440-746, Korea
| | - Kyeong Kyu Kim
- Department of Biology, Massachusetts Institute of Technology77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University300 Chunchundong, Jangangu, Suwon, Kyunggido 440-746, Korea
| | - Ky Lowenhaupt
- Department of Biology, Massachusetts Institute of Technology77 Massachusetts Avenue, Cambridge, MA 02139, USA
- To whom correspondence should be addressed. Tel: +1 617 253 4710; Fax: +1 61 258 8299;
| | - Alexander Rich
- Department of Biology, Massachusetts Institute of Technology77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Ha SC, Van Quyen D, Hwang HY, Oh DB, Brown BA, Lee SM, Park HJ, Ahn JH, Kim KK, Kim YG. Biochemical characterization and preliminary X-ray crystallographic study of the domains of human ZBP1 bound to left-handed Z-DNA. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:320-3. [PMID: 16448869 DOI: 10.1016/j.bbapap.2005.12.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Revised: 12/07/2005] [Accepted: 12/08/2005] [Indexed: 11/16/2022]
Abstract
ZBP1 is involved in host responses against cellular stresses, including tumorigenesis and viral infection. Structurally, it harbors two copies of the Zalpha domain containing the Zalpha motif, at its N terminus. Here, we attempted to characterize the Z-DNA binding activities of two Zalpha domains in the human ZBP1, hZalpha(ZBP1) and hZbeta(ZBP1), using circular dichroism (CD). Our results indicated that both hZalpha(ZBP1) and hZbeta(ZBP1) are viable Z-DNA binders, and their binding activities are comparable to those of previously-established Zalpha domains. Additionally, we crystallized hZbeta(ZBP1) in a complex with Z-DNA, d(TCGCGCG)2. The crystal diffracted to 1.45 angstroms, and belongs to the P2(1)2(1)2(1) space group, with the unit-cell parameters: a = 29.53 angstroms, b = 58.25 angstroms, and c = 88.61 angstroms. The delineation of this structure will provide insight into the manner in which diverse Zalpha motifs recognize Z-DNA.
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Affiliation(s)
- Sung Chul Ha
- Department of Molecular Cell Biology, Center for Molecular Medicine, SBRI, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea
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Athanasiadis A, Placido D, Maas S, Brown BA, Lowenhaupt K, Rich A. The crystal structure of the Zbeta domain of the RNA-editing enzyme ADAR1 reveals distinct conserved surfaces among Z-domains. J Mol Biol 2005; 351:496-507. [PMID: 16023667 DOI: 10.1016/j.jmb.2005.06.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Revised: 06/06/2005] [Accepted: 06/08/2005] [Indexed: 11/20/2022]
Abstract
The Zalpha domains represent a growing subfamily of the winged helix-turn-helix (HTH) domain family whose members share a remarkable ability to bind specifically to Z-DNA and/or Z-RNA. They have been found exclusively in proteins involved in interferon response and, while their importance in determining pox viral pathogenicity has been demonstrated, their actual target and biological role remain obscure. Cellular proteins containing Zalpha domains bear a second homologous domain termed Zbeta, which appears to lack the ability to bind left-handed nucleic acids. Here, we present the crystal structure of the Zbeta domain from the human double-stranded RNA adenosine deaminase ADAR1 at 0.97 A, determined by single isomorphous replacement including anomalous scattering. Zbeta maintains a winged-HTH fold with the addition of a C-terminal helix. Mapping of the Zbeta conservation profile on the Zbeta surface reveals a new conserved surface formed partly by the terminal helix 4, involved in metal binding and dimerization and absent from Zalpha domains. Our results show how two domains similar in fold may have evolved into different functional entities even in the context of the same protein.
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Affiliation(s)
- Alekos Athanasiadis
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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33
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Rothenburg S, Deigendesch N, Dittmar K, Koch-Nolte F, Haag F, Lowenhaupt K, Rich A. A PKR-like eukaryotic initiation factor 2alpha kinase from zebrafish contains Z-DNA binding domains instead of dsRNA binding domains. Proc Natl Acad Sci U S A 2005; 102:1602-7. [PMID: 15659550 PMCID: PMC547857 DOI: 10.1073/pnas.0408714102] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The double-stranded RNA (dsRNA)-dependent protein kinase (PKR) is induced as part of the IFN response in mammals and acts to shut down protein synthesis by the phosphorylation of eukaryotic initiation factor 2alpha (eIF2alpha). In fish, a PKR-like kinase activity has been detected, but the enzyme responsible has eluded characterization. Here, we describe a PKR-like kinase from zebrafish. Phylogenetic analysis shows that the C-terminal kinase domain is more closely related to the kinase domain of PKR than to any of the other three known eIF2alpha kinases. Surprisingly, instead of the two dsRNA binding domains found at the N terminus of PKR, there are two Zalpha domains. Zalpha domains specifically bind dsDNA and RNA in the left-handed Z conformation, often with high affinity. They have been found previously in two other IFN-inducible proteins, the dsRNA editing enzyme, ADAR1, and Z-DNA binding protein 1 (ZBP1), as well as in the poxvirus virulence factor, E3L. This previously undescribed kinase, designated PKZ (protein kinase containing Z-DNA binding domains), is transcribed constitutively at low levels and is highly induced after injection of poly(inosinic)-poly(cytidylic) acid, which simulates viral infection. Binding of Z-DNA by the Zalpha domain of PKZ was demonstrated by circular dichroism. PKZ inhibits translation in transfected cells; site-directed mutagenesis indicates that this inhibition depends on its catalytic activity. Identification of a gene combining Zalpha domains with a PKR-like kinase domain strengthens the hypothesis that the ability to bind left-handed nucleic acid plays a role in the host response to viruses.
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Affiliation(s)
- Stefan Rothenburg
- Institut für Immunologie, Universitätsklinikum Eppendorf, 20246 Hamburg, Germany.
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34
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Fluorescence Detection of Protein/Z-DNA Interactions. B KOREAN CHEM SOC 2004. [DOI: 10.5012/bkcs.2004.25.9.1430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Lushnikov AY, Brown BA, Oussatcheva EA, Potaman VN, Sinden RR, Lyubchenko YL. Interaction of the Zalpha domain of human ADAR1 with a negatively supercoiled plasmid visualized by atomic force microscopy. Nucleic Acids Res 2004; 32:4704-12. [PMID: 15342791 PMCID: PMC516073 DOI: 10.1093/nar/gkh810] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interest to the left-handed DNA conformation has been recently boosted by the findings that a number of proteins contain the Zalpha domain, which has been shown to specifically recognize Z-DNA. The biological function of Zalpha is presently unknown, but it has been suggested that it may specifically direct protein regions of Z-DNA induced by negative supercoiling in actively transcribing genes. Many studies, including a crystal structure in complex with Z-DNA, have focused on the human ADAR1 Zalpha domain in isolation. We have hypothesized that the recognition of a Z-DNA sequence by the Zalpha(ADAR1) domain is context specific, occurring under energetic conditions, which favor Z-DNA formation. To test this hypothesis, we have applied atomic force microscopy to image Zalpha(ADAR1) complexed with supercoiled plasmid DNAs. We have demonstrated that the Zalpha(ADAR1) binds specifically to Z-DNA and preferentially to d(CG)(n) inserts, which require less energy for Z-DNA induction compared to other sequences. A notable finding is that site-specific Zalpha binding to d(GC)(13) or d(GC)(2)C(GC)(10) inserts is observed when DNA supercoiling is insufficient to induce Z-DNA formation. These results indicate that Zalpha(ADAR1) binding facilities the B-to-Z transition and provides additional support to the model that Z-DNA binding proteins may regulate biological processes through structure-specific recognition.
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36
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Wang Q, Carmichael GG. Effects of length and location on the cellular response to double-stranded RNA. Microbiol Mol Biol Rev 2004; 68:432-52, table of contents. [PMID: 15353564 PMCID: PMC515255 DOI: 10.1128/mmbr.68.3.432-452.2004] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Since double-stranded RNA (dsRNA) has not until recently generally been thought to be deliberately expressed in cells, it has commonly been assumed that the major source of cellular dsRNA is viral infections. In this view, the cellular responses to dsRNA would be natural and perhaps ancient antiviral responses. While the cell may certainly react to some dsRNAs as an antiviral response, this does not represent the only response or even, perhaps, the major one. A number of recent observations have pointed to the possibility that dsRNA molecules are not seen only as evidence of viral infection or recognized for degradation because they cannot be translated. In some instances they may also play important roles in normal cell growth and function. The purpose of this review is to outline our current understanding of the fate of dsRNA in cells, with a focus on the apparent fact that their fates and functions appear to depend critically not only on where in the cell dsRNA molecules are found, but also on how long they are and perhaps on how abundant they are.
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Affiliation(s)
- Qiaoqiao Wang
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030-3301, USA
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37
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Borén M, Larsson H, Falk A, Jansson C. The barley starch granule proteome—internalized granule polypeptides of the mature endosperm. PLANT SCIENCE 2004. [PMID: 0 DOI: 10.1016/j.plantsci.2003.10.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
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38
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Kim YG, Lowenhaupt K, Oh DB, Kim KK, Rich A. Evidence that vaccinia virulence factor E3L binds to Z-DNA in vivo: Implications for development of a therapy for poxvirus infection. Proc Natl Acad Sci U S A 2004; 101:1514-8. [PMID: 14757814 PMCID: PMC341766 DOI: 10.1073/pnas.0308260100] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The E3L gene product found in all poxviruses is required for the lethality of mice in vaccinia virus infection. Both the C-terminal region, consisting of a double-stranded RNA-binding motif, and the N-terminal region (vZ(E3L)), which is similar to the Zalpha family of Z-DNA-binding proteins, are required for infection. It has recently been demonstrated that the function of the N-terminal domain depends on its ability to bind Z-DNA; Z-DNA-binding domains from unrelated mammalian proteins fully complement an N-terminal deletion of E3L. Mutations that decrease affinity for Z-DNA have similar effects in decreasing pathogenicity. Compounds that block the Z-DNA-binding activity of E3L may also limit infection by the poxvirus. Here we show both an in vitro and an in vivo assay with the potential to be used in screening for such compounds. Using a conformation-specific yeast one-hybrid assay, we compared the results for Z-DNA binding of vZ(E3L) with those for human Zbeta(ADAR1), a peptide that has similarity to the Zalpha motif but does not bind Z-DNA, and with a mutant of hZbeta(ADAR1), which binds Z-DNA. The results suggest that this system can be used for high-throughput screening.
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Affiliation(s)
- Yang-Gyun Kim
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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39
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Kim YG, Muralinath M, Brandt T, Pearcy M, Hauns K, Lowenhaupt K, Jacobs BL, Rich A. A role for Z-DNA binding in vaccinia virus pathogenesis. Proc Natl Acad Sci U S A 2003; 100:6974-9. [PMID: 12777633 PMCID: PMC165815 DOI: 10.1073/pnas.0431131100] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The N-terminal domain of the E3L protein of vaccinia virus has sequence similarity to a family of Z-DNA binding proteins of defined three-dimensional structure and it is necessary for pathogenicity in mice. When other Z-DNA-binding domains are substituted for the similar E3L domain, the virus retains its lethality after intracranial inoculation. Mutations decreasing Z-DNA binding in the chimera correlate with decreases in viral pathogenicity, as do analogous mutations in wild-type E3L. A chimeric virus incorporating a related protein that does not bind Z-DNA is not pathogenic, but a mutation that creates Z-DNA binding makes a lethal virus. The ability to bind the Z conformation is thus essential to E3L activity. This finding may allow the design of a class of antiviral agents, including agents against variola (smallpox), which has an almost identical E3L.
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Affiliation(s)
- Yang-Gyun Kim
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 68-233, Cambridge, MA 02139-4307, USA
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40
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Oh DB, Kim YG, Rich A. Z-DNA-binding proteins can act as potent effectors of gene expression in vivo. Proc Natl Acad Sci U S A 2002; 99:16666-71. [PMID: 12486233 PMCID: PMC139201 DOI: 10.1073/pnas.262672699] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The role of Z-DNA-binding proteins in vivo is explored in yeast. A conformation-specific yeast one-hybrid system is made in which formation of Z-DNA is studied near a minimal promoter site where it can be stabilized by negative supercoiling in addition to protein binding. Experiments were carried out with a Z-DNA-binding protein domain from the editing enzyme, double-stranded RNA adenosine deaminase 1. In the one-hybrid system, the reporter gene is activated when a Z-DNA-specific binding domain is fused with an activation domain and expressed in vivo. Significantly, it was found that even in the absence of the activation domain there is substantial transcription of the reporter gene if the Z-DNA-binding protein is expressed in the cell. This result suggests that Z-DNA formation in the promoter region induced or stabilized by a Z-DNA-binding protein can act as a cis-element in gene regulation. Related results have been found recently when the human chromatin-remodeling system converts a segment of DNA in the promoter region of the human colony-stimulating factor 1 gene into the left-handed Z-conformation.
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Affiliation(s)
- Doo-Byoung Oh
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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41
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Rothenburg S, Schwartz T, Koch-Nolte F, Haag F. Complex regulation of the human gene for the Z-DNA binding protein DLM-1. Nucleic Acids Res 2002; 30:993-1000. [PMID: 11842111 PMCID: PMC100341 DOI: 10.1093/nar/30.4.993] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dlm-1 is a recently described gene which is upregulated in murine stromal cells lining tumors. The function of the 40 kDa DLM-1 protein is poorly understood. DLM-1 contains an N-terminal Z-DNA binding domain homologous to the Zalpha domain in the RNA editing enzyme ADAR1. We report the cloning of human and rat DLM-1. In addition to the Zalpha domain, three further conserved regions were identified. One of these is homologous to the second Z-DNA binding domain, Zbeta, of ADAR1. We find that human DLM-1 is predominantly expressed in lymphatic tissues. The gene spans 17 kb and consists of 10 exons. DNA transcripts are extremely heterogeneous as a result of alternative splicing and the usage of exon variants combined with at least two transcriptional start sites and 3'-terminal exons. The exon coding for the Zalpha domain was present in approximately one-third of the analyzed mRNAs. Nearly half of the transcripts contained exon variants that had premature stop codons incorporated. Based on our analysis, over 2000 different mRNAs may be produced due to alternative splicing and usage of different 5' and 3' ends. The cellular function of DLM-1 appears to call for a high degree of adaptation by this complex regulation.
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Affiliation(s)
- Stefan Rothenburg
- Institute for Immunology, University Hospital Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg, Germany
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42
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Velten M, Gomez-Vrielynck N, Chaffotte A, Ladjimi MM. Domain structure of the HSC70 cochaperone, HIP. J Biol Chem 2002; 277:259-66. [PMID: 11687574 DOI: 10.1074/jbc.m106881200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The domain structure of the HSC70-interacting protein (HIP), a 43-kDa cytoplasmic cochaperone involved in the regulation of HSC70 chaperone activity and the maturation of progesterone receptor, has been probed by limited proteolysis and biophysical and biochemical approaches. HIP proteolysis by thrombin and chymotrypsin generates essentially two fragments, an NH2-terminal fragment of 25 kDa (N25) and a COOH-terminal fragment of 18 kDa (C18) that appear to be well folded and stable as indicated by circular dichroism and recombinant expression in Escherichia coli. NH2-terminal amino acid sequencing of the respective fragments indicates that both proteases cleave HIP within a predicted alpha-helix following the tetratricopeptide repeat (TPR) region, despite their different specificities and the presence of several potential cleavage sites scattered throughout the sequence, thus suggesting that this region is particularly accessible and may constitute a linker between two structural domains. After size exclusion chromatography, N25 and C18 elute as two distinct and homogeneous species having a Stokes radius of 49 and 24 A, respectively. Equilibrium sedimentation and sedimentation velocity indicate that N25 is a stable dimer, whereas C18 is monomeric in solution, with sedimentation coefficients of 3.2 and 2.3 S and f/f(o) values of 1.5 and 1.1 for N25 and C18, respectively, indicating that the N25 is elongated whereas C18 is globular in shape. Both domains are able to bind to the ATPase domain of HSC70 and inhibit rhodanese aggregation. Moreover, their effects appear to be additive when used in combination, suggesting a cooperation of these domains in the full-length protein not only for HSC70 binding but also for chaperone activity. Altogether, these results indicate that HIP is made of two structural and functional domains, an NH2-terminal 25-kDa domain, responsible for the dimerization and the overall asymmetry of the molecule, and a COOH-terminal 18-kDa globular domain, both involved in HSC70 and unfolded protein binding.
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Affiliation(s)
- Marion Velten
- Laboratoire de Biochimie des Signaux Régulateurs Cellulaires et Moléculaires, UMR 7631, CNRS-Université Pierre et Marie Curie, 96 Boulevard Raspail and Institut Pasteur, 28 rue du Dr. Roux, Paris, France
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43
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Abstract
Tremendous progress has been made in understanding the molecular basis of the antiviral actions of interferons (IFNs), as well as strategies evolved by viruses to antagonize the actions of IFNs. Furthermore, advances made while elucidating the IFN system have contributed significantly to our understanding in multiple areas of virology and molecular cell biology, ranging from pathways of signal transduction to the biochemical mechanisms of transcriptional and translational control to the molecular basis of viral pathogenesis. IFNs are approved therapeutics and have moved from the basic research laboratory to the clinic. Among the IFN-induced proteins important in the antiviral actions of IFNs are the RNA-dependent protein kinase (PKR), the 2',5'-oligoadenylate synthetase (OAS) and RNase L, and the Mx protein GTPases. Double-stranded RNA plays a central role in modulating protein phosphorylation and RNA degradation catalyzed by the IFN-inducible PKR kinase and the 2'-5'-oligoadenylate-dependent RNase L, respectively, and also in RNA editing by the IFN-inducible RNA-specific adenosine deaminase (ADAR1). IFN also induces a form of inducible nitric oxide synthase (iNOS2) and the major histocompatibility complex class I and II proteins, all of which play important roles in immune response to infections. Several additional genes whose expression profiles are altered in response to IFN treatment and virus infection have been identified by microarray analyses. The availability of cDNA and genomic clones for many of the components of the IFN system, including IFN-alpha, IFN-beta, and IFN-gamma, their receptors, Jak and Stat and IRF signal transduction components, and proteins such as PKR, 2',5'-OAS, Mx, and ADAR, whose expression is regulated by IFNs, has permitted the generation of mutant proteins, cells that overexpress different forms of the proteins, and animals in which their expression has been disrupted by targeted gene disruption. The use of these IFN system reagents, both in cell culture and in whole animals, continues to provide important contributions to our understanding of the virus-host interaction and cellular antiviral response.
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Affiliation(s)
- C E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9610, USA.
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44
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Heiring C, Muller YA. Folding screening assayed by proteolysis: application to various cystine deletion mutants of vascular endothelial growth factor. PROTEIN ENGINEERING 2001; 14:183-8. [PMID: 11342715 DOI: 10.1093/protein/14.3.183] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The production of recombinant proteins in Escherichia coli often leads to the formation of inclusion bodies. Although this has a number of advantages, a major disadvantage is the need to develop folding protocols for the renaturing of the proteins. However, the systematic screening of folding conditions is often hampered by the lack of convenient assays to detect correctly folded proteins. To address this problem we present a simple protocol, which combines folding screens and limited proteolysis to rapidly assess and optimize folding conditions. The efficacy of this method, termed FSAP (folding screening assayed by proteolysis), is demonstrated by the large-scale folding, purification and crystallization of various cystine deletion mutants of the cystine knot family member: vascular endothelial growth factor (VEGF). These mutants are particularly difficult to fold as the cystine knot is believed to make major contributions to the stability of the protein and this family of proteins lacks extensive hydrophobic core regions.
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Affiliation(s)
- C Heiring
- Forschungsgruppe Kristallographie, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, D-13092 Berlin, Germany
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45
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Brown BA, Lowenhaupt K, Wilbert CM, Hanlon EB, Rich A. The zalpha domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA. Proc Natl Acad Sci U S A 2000; 97:13532-6. [PMID: 11087828 PMCID: PMC17610 DOI: 10.1073/pnas.240464097] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Zalpha domain of human double-stranded RNA adenosine deaminase 1 binds specifically to left-handed Z-DNA and stabilizes the Z-conformation. Here we report spectroscopic and analytical results that demonstrate that Zalpha can also stabilize the left-handed Z-conformation in double-stranded RNA. Zalpha induces a slow transition from the right-handed A-conformation to the Z-form in duplex r(CG)(6), with an activation energy of 38 kcal mol(-1). We conclude that Z-RNA as well as Z-DNA can be accommodated in the tailored binding site of Zalpha. The specific binding of Z-RNA by Zalpha may be involved in targeting double-stranded RNA adenosine deaminase 1 for a role in hypermutation of RNA viruses.
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Affiliation(s)
- B A Brown
- Department of Biology and George R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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46
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Kim YG, Lowenhaupt K, Maas S, Herbert A, Schwartz T, Rich A. The Zab Domain of the Human RNA Editing Enzyme ADAR1 Recognizes Z-DNA When Surrounded by B-DNA. J Biol Chem 2000. [DOI: 10.1016/s0021-9258(19)61450-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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47
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Slavov D, Crnogorac-Jurcević T, Clark M, Gardiner K. Comparative analysis of the DRADA A-to-I RNA editing gene from mammals, pufferfish and zebrafish. Gene 2000; 250:53-60. [PMID: 10854778 DOI: 10.1016/s0378-1119(00)00175-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The DRADA gene in mammals encodes an A-to-I RNA editase, an adenosine deaminase that acts on pre-mRNAs to produce site specific inosines. DRADA has been shown to deaminate specific adenosine residues in a subset of glutamate and serotonin receptors, and this editing results in proteins of altered sequences and functional properties. DRADA thus plays a role in creating protein diversity. To study the evolutionary significance of this gene, we have characterized the genomic structure of DRADA from Fugu rubripes, and compared the protein sequences of DRADA from mammals, pufferfish and zebrafish. The DRADA gene from Fugu is three-fold compacted with respect to the human gene, and contains a novel intron within the large second coding exon. DRADA cDNAs were isolated from zebrafish and a second pufferfish, Tetraodon fluviatilis. Comparisons among fish, and between fish and mammals, of the protein sequences show that the catalytic domains are highly conserved for each gene, while the RNA binding domains vary within a single protein in their levels of conservation. Conservation within the Z DNA binding domain has also been assessed. Different levels of conservation among domains of different functional roles may reflect differences in editase substrate specificity and/or substrate sequence conservation.
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Affiliation(s)
- D Slavov
- Eleanor Roosevelt Institute, Denver, CO, USA
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48
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Weiss C, Oppliger W, Vergères G, Demel R, Jenö P, Horst M, de Kruijff B, Schatz G, Azem A. Domain structure and lipid interaction of recombinant yeast Tim44. Proc Natl Acad Sci U S A 1999; 96:8890-4. [PMID: 10430866 PMCID: PMC17703 DOI: 10.1073/pnas.96.16.8890] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane. It functions as a membrane anchor for the ATP-driven protein import motor whose other subunits are the mitochondrial 70-kDa heat-shock protein (mhsp70) and its nucleotide exchange factor, mGrpE. To understand how this motor is anchored to the inner membrane, we have overexpressed Tim44 in Escherichia coli and studied the properties of the pure protein and its interaction with model lipid membranes. Limited proteolysis and analytical ultracentrifugation indicate that Tim44 is an elongated monomer with a stably folded C-terminal domain. The protein binds strongly to liposomes composed of phosphatidylcholine and cardiolipin but only weakly to liposomes containing phosphatidylcholine alone. Studies with phospholipid monolayers suggest that Tim44 binds to phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region.
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Affiliation(s)
- C Weiss
- Department of Biochemistry, Tel-Aviv University, Tel-Aviv 69978, Israel
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49
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Kim YG, Lowenhaupt K, Schwartz T, Rich A. The interaction between Z-DNA and the Zab domain of double-stranded RNA adenosine deaminase characterized using fusion nucleases. J Biol Chem 1999; 274:19081-6. [PMID: 10383410 DOI: 10.1074/jbc.274.27.19081] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Zab is a structurally defined protein domain that binds specifically to DNA in the Z conformation. It consists of amino acids 133-368 from the N terminus of human double-stranded RNA adenosine deaminase, which is implicated in RNA editing. Zab contains two motifs with related sequence, Zalpha and Zbeta. Zalpha alone is capable of binding Z-DNA with high affinity, whereas Zbeta alone has little DNA binding activity. Instead, Zbeta modulates Zalpha binding, resulting in increased sequence specificity for alternating (dCdG)n as compared with (dCdA/dTdG)n. This relative specificity has previously been demonstrated with short oligonucleotides. Here we demonstrate that Zab can also bind tightly to (dCdG)n stabilized in the Z form in supercoiled plasmids. Binding was assayed by monitoring cleavage of the plasmids using fusion nucleases, in which Z-DNA-binding peptides from the N terminus of double-stranded RNA adenosine deaminase are linked to the nuclease domain of FokI. A fusion nuclease containing Zalpha shows less sequence specificity, as well as less conformation specificity, than one containing Zab. Further, a construct in which Zbeta has been replaced in Zab with Zalpha, cleaves Z-DNA regions in supercoiled plasmids more efficiently than the wild type but with little sequence specificity. We conclude that in the Zab domain, both Zalpha and Zbeta contact DNA. Zalpha contributes contacts that produce conformation specificity but not sequence specificity. In contrast, Zbeta contributes weakly to binding affinity but discriminates between sequences of Z-DNAs.
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Affiliation(s)
- Y G Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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50
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Schwartz T, Rould MA, Lowenhaupt K, Herbert A, Rich A. Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science 1999; 284:1841-5. [PMID: 10364558 DOI: 10.1126/science.284.5421.1841] [Citation(s) in RCA: 298] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The editing enzyme double-stranded RNA adenosine deaminase includes a DNA binding domain, Zalpha, which is specific for left-handed Z-DNA. The 2.1 angstrom crystal structure of Zalpha complexed to DNA reveals that the substrate is in the left-handed Z conformation. The contacts between Zalpha and Z-DNA are made primarily with the "zigzag" sugar-phosphate backbone, which provides a basis for the specificity for the Z conformation. A single base contact is observed to guanine in the syn conformation, characteristic of Z-DNA. Intriguingly, the helix-turn-helix motif, frequently used to recognize B-DNA, is used by Zalpha to contact Z-DNA.
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Affiliation(s)
- T Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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