Structural Analyses of Zinc Finger Domains for Specific Interactions with DNA Ki Seong Eom1, Jin Sung Cheong2,3, and Seung Jae Lee3*

Total Page:16

File Type:pdf, Size:1020Kb

Structural Analyses of Zinc Finger Domains for Specific Interactions with DNA Ki Seong Eom1, Jin Sung Cheong2,3, and Seung Jae Lee3* J. Microbiol. Biotechnol. (2016), 26(12), 2019–2029 http://dx.doi.org/10.4014/jmb.1609.09021 Research Article Review jmb Structural Analyses of Zinc Finger Domains for Specific Interactions with DNA Ki Seong Eom1, Jin Sung Cheong2,3, and Seung Jae Lee3* 1Department of Neurosurgery, School of Medicine and Hospital, Wonkwang University, Iksan 54538, Republic of Korea 2Department of Neurology, School of Medicine and Hospital, Wonkwang University, Iksan 54538, Republic of Korea 3Department of Chemistry and Research Institute of Physic and Chemistry, Chonbuk National University, Jeonju 54896, Republic of Korea Received: September 19, 2016 Revised: September 26, 2016 Zinc finger proteins are among the most extensively applied metalloproteins in the field of Accepted: September 28, 2016 biotechnology owing to their unique structural and functional aspects as transcriptional and translational regulators. The classical zinc fingers are the largest family of zinc proteins and they provide critical roles in physiological systems from prokaryotes to eukaryotes. Two First published online cysteine and two histidine residues (Cys2His2) coordinate to the zinc ion for the structural October 6, 2016 functions to generate a ββα fold, and this secondary structure supports specific interactions *Corresponding author with their binding partners, including DNA, RNA, lipids, proteins, and small molecules. In Phone: +82-63-270-3412; this account, the structural similarity and differences of well-known Cys2His2-type zinc fingers Fax: +82-63-260-3407; such as zinc interaction factor 268 (ZIF268), transcription factor IIIA (TFIIIA), GAGA, and Ros E-mail: [email protected] will be explained. These proteins perform their specific roles in species from archaea to eukaryotes and they show significant structural similarity; however, their aligned amino acids present low sequence homology. These zinc finger proteins have different numbers of domains for their structural roles to maintain biological progress through transcriptional regulations from exogenous stresses. The superimposed structures of these finger domains provide interesting details when these fingers are applied to specific gene binding and editing. The structural information in this study will aid in the selection of unique types of zinc finger applications in vivo and in vitro approaches, because biophysical backgrounds including pISSN 1017-7825, eISSN 1738-8872 complex structures and binding affinities aid in the protein design area. Copyright© 2016 by The Korean Society for Microbiology Keywords: Zinc finger proteins, metalloproteins, classical zinc finger, transcriptional regulator and Biotechnology Introduction 57, 68]. Early studies of zinc fingers have been limited to DNA binding ability and its transcriptional regulation, but One of the most well-known groups of transcriptional recent applications of zinc fingers in various fields are of factors in eukaryotes is the zinc finger proteins, which major interest owing to their specific interactions for coordinate zinc ions to achieve a folded structure that is cognate DNA, RNA, proteins, lipids, and small molecules crucial for interactions with its binding partners in through hydrogen bonds and hydrophobic interactions [32, physiological systems [20, 34, 36, 38-40, 43, 48, 51, 68]. 43, 56, 68]. The binding affinities of zinc fingers to their Biochemical and biophysical studies of these metalloproteins binding partners are significantly high, and preliminary have focused on eukaryotes owing to their critical functions reports proved that these proteins bind to their specific in signaling cascades. The growing evidence and genomic nucleic acids with sub-nanomolar ranges of dissociation advances proved that zinc fingers perform crucial roles in constants (Kd). The elaborate control of transcriptional maintaining physiological processes from prokaryotes to regulation is triggered by this tight binding, and gene eukaryotes, including the plant kingdom [2, 28, 31, 42, 52, expression is up-regulated through this complex generation December 2016 ⎪ Vol. 26⎪ No. 12 2020 Eom et al. [16, 29, 54]. Primary Structures of the Cys2His2-Type Zinc Structural domains of zinc fingers have been applied to Finger Motif gene-editing technologies to improve low specificity in vitro and in vivo for the use of clinical trials in the last decade Classical Zinc Finger Domains and Metal Coordination [20, 48, 74]. This technology has received considerable The zinc finger domain coordinates to cysteine (Cys) and attention because zinc fingers can improve specific binding histidine (His) side chains, and the secondary structure is abilities to target nucleic acids as a part of nucleases. Most generated only in the presence of the zinc ion (Zn2+). This zinc finger proteins have more than one domain, and many metal ion is structurally important in generating the biophysical reports proved that one zinc finger domain is secondary structure of both classical (Cys2His2) and not enough to obtain specific bindings [60, 76], although nonclassical (other zinc coordinating combinations except one GAGA binding domain from Drosophila has a Cys2His2) zinc fingers [17, 34, 43, 49, 61, 66, 68]. Two β- significantly high binding affinity to its cognate sequence strands and one α-helix is a general zinc finger domain of DNA [53]. To understand these tight bindings at the from classical zinc fingers (Fig. 1). Zinc interacting factor atomic level, interaction details of zinc fingers have been 268 (ZIF268), a member of the classical zinc finger group widely studied using nuclear magnetic resonance (NMR) and a transcriptional regulator, has three zinc finger and X-ray crystallography techniques. Unfortunately, the domains, and their interaction details were studied by gel structures of zinc fingers still need to be investigated mobile shift assay and X-ray crystallography [3, 4, 25, 62]. because of the limited solubility of full sequences of zinc The three zinc fingers generate tight binding compared finger proteins and difficulties of crystallization. Many zinc with that of one zinc finger domain, as is present in other fingers have limited solubility due to zinc finger domains zinc finger proteins. Many approaches were applied to and other parts of the proteins, and this limited solubility modify genes in the last decade, and these classical zinc retards structural and functional studies. fingers are extensively applied to biotechnology in the field In this account, the authors would like to discuss of gene editing. For these reasons, ZIF268 was applied to interaction details of Cys2His2-type zinc finger domains control site-specific DNA interactions as binding domains based on structural features that are widely studied and applied to recent advances in biotechnologies. There are growing reports of zinc finger domains in most kingdoms, including archaic, prokaryotic, and eukaryotic species, and their physiological and biochemical features need to be discovered for successful applications in terms of biotechnologies, including gene editing, therapeutic targets, alteration of enzymatic pathways, and improving the yields of specific metabolites. The zinc ion is a structural factor in zinc finger proteins that regulates transcriptional and translational pathways [38, 43]. These structural domains are essential in biological systems, including normal processes to maintain routine pathways and to respond to specific signals that can be artificially controlled based on the primary to quaternary structures of these domains. Cys2His2-type domains have been extensively and intensely investigated over the last three decades in order to understand their binding events and affinity against their cognate binding partners. This article will further Classical zinc finger domain (Cys His -type) coordinates compare the structural aspects of various zinc finger domains, Fig. 1. 2 2 with the zinc ion (cyan ball), and the secondary structures are from metal coordination to nucleic acid interactions. The generated rapidly. structural similarity and sequence variations are reviewed Four residues, Cys107, Cys112, His125, and His 129, coordinate to the to give valuable information for the selection and zinc ion with tetrahedral geometry. The first zinc finger domain from application of suitable candidates among zinc fingers for synthesized ZIF268 coordinates with the zinc ion to form a ββα structure bioengineering. to interact with dsDNA (PDB accession: 4X9J) through an α-helix. J. Microbiol. Biotechnol. Structural Analyses of Zinc Finger Domains for Specific Interactions with DNA 2021 including zinc finger nucleases (ZFN) and transcription The structural and functional studies of nonclassical zinc activator-like effector nucleases (TALENs) [5, 27, 48]. finger domains showed many interesting aspects based on Although cleavage domains have powerful activity, they the combinations of Cys and His residues such as Cys4, should recognize specific sequences to perform their Cys3His1, Cys1His3, and Cys2His1(His1)Cys1 types of zinc cleavages to their target DNAs. These applications of finger domains [43, 54, 68]. binding domains have powerful advantages in terms of safety and toxicity when they are applied to in vivo systems. Structures of Classical Zinc Fingers The zinc ion generates tetrahedral geometry (Td) rapidly Classical zinc fingers are the largest family among zinc when it is applied to the apo-zinc finger domain in vitro finger proteins, and a single domain usually has 28-30 system to recognize target DNA
Recommended publications
  • Role of CCCH-Type Zinc Finger Proteins in Human Adenovirus Infections
    viruses Review Role of CCCH-Type Zinc Finger Proteins in Human Adenovirus Infections Zamaneh Hajikhezri 1, Mahmoud Darweesh 1,2, Göran Akusjärvi 1 and Tanel Punga 1,* 1 Department of Medical Biochemistry and Microbiology, Uppsala University, 75123 Uppsala, Sweden; [email protected] (Z.H.); [email protected] (M.D.); [email protected] (G.A.) 2 Department of Microbiology and Immunology, Al-Azhr University, Assiut 11651, Egypt * Correspondence: [email protected]; Tel.: +46-733-203-095 Received: 28 October 2020; Accepted: 16 November 2020; Published: 18 November 2020 Abstract: The zinc finger proteins make up a significant part of the proteome and perform a huge variety of functions in the cell. The CCCH-type zinc finger proteins have gained attention due to their unusual ability to interact with RNA and thereby control different steps of RNA metabolism. Since virus infections interfere with RNA metabolism, dynamic changes in the CCCH-type zinc finger proteins and virus replication are expected to happen. In the present review, we will discuss how three CCCH-type zinc finger proteins, ZC3H11A, MKRN1, and U2AF1, interfere with human adenovirus replication. We will summarize the functions of these three cellular proteins and focus on their potential pro- or anti-viral activities during a lytic human adenovirus infection. Keywords: human adenovirus; zinc finger protein; CCCH-type; ZC3H11A; MKRN1; U2AF1 1. Zinc Finger Proteins Zinc finger proteins are a big family of proteins with characteristic zinc finger (ZnF) domains present in the protein sequence. The ZnF domains consists of various ZnF motifs, which are short 30–100 amino acid sequences, coordinating zinc ions (Zn2+).
    [Show full text]
  • Engineering Zinc-Finger Protein and CRISPR/Cas9 Constructs to Model the Epigenetic and Transcriptional Phenomena That Underlie Cocaine-Related Behaviors
    Engineering zinc-finger protein and CRISPR/Cas9 constructs to model the epigenetic and transcriptional phenomena that underlie cocaine-related behaviors Hamilton PJ, Heller EA, Ortiz Torres I, Burek DD, Lombroso SI, Pirpinias ST, Neve RL, Nestler EJ Multiple studies have implicated genome-wide epigenetic remodeling events in brain reward regions following drug exposure. However, only recently has it become possible to target a given type of epigenetic remodeling to a single gene of interest, in order to probe the causal relationship between such regulation and neuropsychiatric disease (Heller et al., Nat Neurosci, 2014). Our group has successfully utilized synthetic zinc- finger proteins (ZFPs), fused to either the transcriptional repressor, G9a, that promotes histone methylation or the transcriptional activator, p65, that promotes histone acetylation, to determine the behavioral effects of targeted in vivo epigenetic reprogramming in a locus-specific and cell-type specific manner. Given the success of our ZFP approaches, we have broadened our technical repertoire to include the more novel and flexible CRISPR/Cas9 technology. We designed guide RNAs to target nuclease-dead Cas9 (dCas9) fused to effector domains to the fosB gene locus, a locus heavily implicated in the pathogenesis of drug abuse. We observe that dCas9 fused to the transcriptional activator, VP64, or the transcriptional repressor, KRAB, and targeted to specific sites in the fosB promoter is sufficient to regulate FosB and ΔFosB mRNA levels, in both cultured cells and in the nucleus accumbens (NAc) of mice receiving viral delivery of CRISPR constructs. Next, we designed a fusion construct linking the dCas9 moiety to a pseudo-phosphorylated isoform of the transcription factor CREB (dCas9­ CREB(S133D)).
    [Show full text]
  • XIAP's Profile in Human Cancer
    biomolecules Review XIAP’s Profile in Human Cancer Huailu Tu and Max Costa * Department of Environmental Medicine, Grossman School of Medicine, New York University, New York, NY 10010, USA; [email protected] * Correspondence: [email protected] Received: 16 September 2020; Accepted: 25 October 2020; Published: 29 October 2020 Abstract: XIAP, the X-linked inhibitor of apoptosis protein, regulates cell death signaling pathways through binding and inhibiting caspases. Mounting experimental research associated with XIAP has shown it to be a master regulator of cell death not only in apoptosis, but also in autophagy and necroptosis. As a vital decider on cell survival, XIAP is involved in the regulation of cancer initiation, promotion and progression. XIAP up-regulation occurs in many human diseases, resulting in a series of undesired effects such as raising the cellular tolerance to genetic lesions, inflammation and cytotoxicity. Hence, anti-tumor drugs targeting XIAP have become an important focus for cancer therapy research. RNA–XIAP interaction is a focus, which has enriched the general profile of XIAP regulation in human cancer. In this review, the basic functions of XIAP, its regulatory role in cancer, anti-XIAP drugs and recent findings about RNA–XIAP interactions are discussed. Keywords: XIAP; apoptosis; cancer; therapeutics; non-coding RNA 1. Introduction X-linked inhibitor of apoptosis protein (XIAP), also known as inhibitor of apoptosis protein 3 (IAP3), baculoviral IAP repeat-containing protein 4 (BIRC4), and human IAPs like protein (hILP), belongs to IAP family which was discovered in insect baculovirus [1]. Eight different IAPs have been isolated from human tissues: NAIP (BIRC1), BIRC2 (cIAP1), BIRC3 (cIAP2), XIAP (BIRC4), BIRC5 (survivin), BIRC6 (apollon), BIRC7 (livin) and BIRC8 [2].
    [Show full text]
  • TRAF5, a Novel Tumor Necrosis Factor Receptor-Associated Factor Family
    Proc. Natl. Acad. Sci. USA Vol. 93, pp. 9437-9442, September 1996 Biochemistry TRAF5, a novel tumor necrosis factor receptor-associated factor family protein, mediates CD40 signaling (signal transduction/protein-protein interaction/yeast two-hybrid system) TAKAoMI ISHIDA*, TADASHI ToJo*, TSUTOMU AOKI*, NORIHIKO KOBAYASHI*, TSUKASA OHISHI*, TOSHIKI WATANABEt, TADASHI YAMAMOTO*, AND JUN-ICHIRO INOUE*t Departments of *Oncology and tPathology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108, Japan Communicated by David Baltimore, Massachusetts Institute of Technology, Cambridge, MA, May 22, 1996 (received for review March 8, 1996) ABSTRACT Signals emanating from CD40 play crucial called a death domain, suggesting that these receptors could roles in B-cell function. To identify molecules that transduce have either common or similar signaling mechanisms (13). CD40 signalings, we have used the yeast two-hybrid system to Biochemical purification of receptor-associated proteins or the clone cDNAs encoding proteins that bind the cytoplasmic tail recently developed cDNA cloning system that uses yeast of CD40. A cDNA encoding a putative signal transducer genetic selection led to the discovery of two groups of signal protein, designated TRAF5, has been molecularly cloned. transducer molecules. Members of the first group are proteins TRAF5 has a tumor necrosis factor receptor-associated factor with a TRAF domain for TNFR2 and CD40 such as TRAF1, (TRAF) domain in its carboxyl terminus and is most homol- TRAF2 (17), and TRAF3, also known as CD40bp, LAP-1, or ogous to TRAF3, also known as CRAF1, CD40bp, or LAP-1, CRAF1 or CD40 receptor-associated factor (18-20).
    [Show full text]
  • RING-Type E3 Ligases: Master Manipulators of E2 Ubiquitin-Conjugating Enzymes and Ubiquitination☆
    Biochimica et Biophysica Acta 1843 (2014) 47–60 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbamcr Review RING-type E3 ligases: Master manipulators of E2 ubiquitin-conjugating enzymes and ubiquitination☆ Meredith B. Metzger a,1, Jonathan N. Pruneda b,1, Rachel E. Klevit b,⁎, Allan M. Weissman a,⁎⁎ a Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, 1050 Boyles Street, Frederick, MD 21702, USA b Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195, USA article info abstract Article history: RING finger domain and RING finger-like ubiquitin ligases (E3s), such as U-box proteins, constitute the vast Received 5 March 2013 majority of known E3s. RING-type E3s function together with ubiquitin-conjugating enzymes (E2s) to medi- Received in revised form 23 May 2013 ate ubiquitination and are implicated in numerous cellular processes. In part because of their importance in Accepted 29 May 2013 human physiology and disease, these proteins and their cellular functions represent an intense area of study. Available online 6 June 2013 Here we review recent advances in RING-type E3 recognition of substrates, their cellular regulation, and their varied architecture. Additionally, recent structural insights into RING-type E3 function, with a focus on im- Keywords: RING finger portant interactions with E2s and ubiquitin, are reviewed. This article is part of a Special Issue entitled: U-box Ubiquitin–Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf. Ubiquitin ligase (E3) Published by Elsevier B.V. Ubiquitin-conjugating enzyme (E2) Protein degradation Catalysis 1.
    [Show full text]
  • The Role of ND10 Nuclear Bodies in Herpesvirus Infection: a Frenemy for the Virus?
    viruses Review The Role of ND10 Nuclear Bodies in Herpesvirus Infection: A Frenemy for the Virus? Behdokht Jan Fada, Eleazar Reward and Haidong Gu * Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA; [email protected] (B.J.F.); [email protected] (E.R.) * Correspondence: [email protected]; Tel.: +1-313-577-6402 Abstract: Nuclear domains 10 (ND10), a.k.a. promyelocytic leukemia nuclear bodies (PML-NBs), are membraneless subnuclear domains that are highly dynamic in their protein composition in response to cellular cues. They are known to be involved in many key cellular processes including DNA damage response, transcription regulation, apoptosis, oncogenesis, and antiviral defenses. The diversity and dynamics of ND10 residents enable them to play seemingly opposite roles under different physiological conditions. Although the molecular mechanisms are not completely clear, the pro- and anti-cancer effects of ND10 have been well established in tumorigenesis. However, in herpesvirus research, until the recently emerged evidence of pro-viral contributions, ND10 nuclear bodies have been generally recognized as part of the intrinsic antiviral defenses that converge to the incoming viral DNA to inhibit the viral gene expression. In this review, we evaluate the newly discov- ered pro-infection influences of ND10 in various human herpesviruses and analyze their molecular foundation along with the traditional antiviral functions of ND10. We hope to shed light on the explicit role of ND10 in both the lytic and latent cycles of herpesvirus infection, which is imperative to the delineation of herpes pathogenesis and the development of prophylactic/therapeutic treatments for herpetic diseases.
    [Show full text]
  • Comprehensive Genome-Wide Exploration of C2H2 Zinc Finger Family in Grapevine (Vitis Vinifera L.): Insights Into the Roles in the Pollen Development Regulation
    G C A T T A C G G C A T genes Article Comprehensive Genome-Wide Exploration of C2H2 Zinc Finger Family in Grapevine (Vitis vinifera L.): Insights into the Roles in the Pollen Development Regulation Oscar Arrey-Salas 1,* , José Carlos Caris-Maldonado 2, Bairon Hernández-Rojas 3 and Enrique Gonzalez 1 1 Laboratorio de Genómica Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile; [email protected] 2 Center for Research and Innovation (CRI), Viña Concha y Toro, Ruta k-650 km 10, 3550000 Pencahue, Chile; [email protected] 3 Ph.D Program in Sciences Mention in Modeling of Chemical and Biological Systems, Faculty of Engineering, University of Talca, Calle 1 Poniente, 1141, 3462227 Talca, Chile; [email protected] * Correspondence: [email protected] Abstract: Some C2H2 zinc-finger proteins (ZFP) transcription factors are involved in the development of pollen in plants. In grapevine (Vitis vinifera L.), it has been suggested that abnormalities in pollen development lead to the phenomenon called parthenocarpy that occurs in some varieties of this cultivar. At present, a network involving several transcription factors types has been revealed and key roles have been assigned to members of the C2H2 zinc-finger proteins (ZFP) family in model plants. However, particularities of the regulatory mechanisms controlling pollen formation in grapevine Citation: Arrey-Salas, O.; remain unknown. In order to gain insight into the participation of ZFPs in grapevine gametophyte Caris-Maldonado, J.C.; development, we performed a genome-wide identification and characterization of genes encoding Hernández-Rojas, B.; Gonzalez, E. ZFP (VviZFP family).
    [Show full text]
  • The RING Finger Domain of Varicella-Zoster Virus Orf61p Has
    JOURNAL OF VIROLOGY, July 2010, p. 6861–6865 Vol. 84, No. 13 0022-538X/10/$12.00 doi:10.1128/JVI.00335-10 Copyright © 2010, American Society for Microbiology. All Rights Reserved. NOTES The RING Finger Domain of Varicella-Zoster Virus ORF61p Has E3 Ubiquitin Ligase Activity That Is Essential for Efficient Autoubiquitination and Dispersion of Sp100-Containing Nuclear Bodiesᰔ Matthew S. Walters,† Christos A. Kyratsous,† and Saul J. Silverstein* Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, 701 W. 168th St., New York, New York 10032 Received 12 February 2010/Accepted 6 April 2010 Varicella zoster virus encodes an immediate-early (IE) protein termed ORF61p that is orthologous to the Downloaded from herpes simplex virus IE protein ICP0. Although these proteins share several functional properties, ORF61p does not fully substitute for ICP0. The greatest region of similarity between these proteins is a RING finger domain. We demonstrate that disruption of the ORF61p RING finger domain by amino acid substitution (Cys19Gly) alters ORF61p intranuclear distribution and abolishes ORF61p-mediated dispersion of Sp100- containing nuclear bodies. In addition, we demonstrate that an intact ORF61p RING finger domain is necessary for E3 ubiquitin ligase activity and is required for autoubiquitination and regulation of protein jvi.asm.org stability. Varicella-zoster virus (VZV) and herpes simplex virus type in other ORF61p activities. Therefore, this study was designed at COLUMBIA UNIVERSITY on June 8, 2010 1 (HSV-1) are distantly related alphaherpesviruses. VZV en- to further characterize the ORF61p RING finger domain. codes an immediate-early (IE) protein termed ORF61p that is To extend our understanding of the ORF61p RING finger an ortholog of ICP0, an HSV-1 IE protein (14, 18).
    [Show full text]
  • A New C2H 2 Zinc Finger Protein and a C2C2 Steroid Receptor-Like Component
    Downloaded from genesdev.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press Proteins that bind to Drosophila chorion cis-regulatory elements: A new C2H 2 zinc finger protein and a C2C2 steroid receptor-like component Martin J. Shea, 1 Dennis L. King, 1 Michael J. Conboy, 2 Brian D. Mariani, 3 and Fotis C. Kafatos 1,3 ~Department of Cellular and Developmental Biology, Harvard University Biological Laboratories, Cambridge, Massachusetts 02138 USA; ZJefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania 19107 USA; 3Institute of Molecular Biology and Biotechnology, Research Center of Crete, and Department of Biology, University of Crete, Heraklion 711 10, Crete, Greece Gel mobility-shift assays have been used to identify proteins that bind specifically to the promoter region of the Drosophila s15 chorion gene. These proteins are present in nuclear extracts of ovarian follicles, the tissue where s15 is expressed during development, and bind to specific elements of the promoter that have been shown by transformation analysis to be important for in vivo expression. The DNA binding specificity has been used for molecular cloning of two components from expression cDNA libraries and for their tentative identification with specific DNA-binding proteins of the nuclear extracts. The mRNAs for both of these components, CF1 and CF2, are differentially enriched in the follicles. DNA sequence analysis suggests that both CF1 and CF2 are novel Drosophila transcription factors. CF2 is a member of the C2H2 family of zinc finger proteins, whereas CF1 is a member of the family of steroid hormone receptors. The putative DNA-binding domain of CF1 is highly similar to the corresponding domains of certain vertebrate hormone receptors and recognizes a region of DNA with similar, hyphenated palindromic sequences.
    [Show full text]
  • Zinc Finger Proteins: Getting a Grip On
    Zinc finger proteins: getting a grip on RNA Raymond S Brown C2H2 (Cys-Cys-His-His motif) zinc finger proteins are members others, such as hZFP100 (C2H2) [11] and tristetraprolin of a large superfamily of nucleic-acid-binding proteins in TTP (CCCH) [12], are involved in histone pre-mRNA eukaryotes. On the basis of NMR and X-ray structures, we processing and the degradation of tumor necrosis factor know that DNA sequence recognition involves a short a helix a mRNA, respectively. In addition, there are reports of bound to the major groove. Exactly how some zinc finger dual RNA/DNA-binding proteins, such as the thyroid proteins bind to double-stranded RNA has been a complete hormone receptor (CCCC) [13] and the trypanosome mystery for over two decades. This has been resolved by the poly-zinc finger PZFP1 pre-mRNA processing protein long-awaited crystal structure of part of the TFIIIA–5S RNA (CCHC) [14]. Whether their interactions with RNA are complex. A comparison can be made with identical fingers in a based on the same mechanisms as protein–DNA binding TFIIIA–DNA structure. Additionally, the NMR structure of is an intriguing structural question that has remained TIS11d bound to an AU-rich element reveals the molecular unanswered until now. details of the interaction between CCCH fingers and single-stranded RNA. Together, these results contrast the What follows is an attempt to expose both similarities different ways that zinc finger proteins bind with high and differences between C2H2 zinc finger protein bind- specificity to their RNA targets. ing to RNA and DNA based on recent X-ray structures.
    [Show full text]
  • Exogenous PPAR 2 but Not PPAR 1 Reactivates Adipogenesis
    Downloaded from genesdev.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH COMMUNICATION ␥ differential isoform function. Rationally engineered PPAR knockdown by transcription factors potentially provide a powerful tool engineered transcription for targeted regulation of endogenous genes by combin- ing a functional transcription regulatory domain with a factors: exogenous PPAR␥2 customized DNA binding domain that can bind to a spe- but not PPAR␥1 cific sequence within the target gene. C2H2 zinc finger proteins (ZFPs) can be engineered to bind with high reactivates adipogenesis specificity to wide a diversity of DNA sequences (Des- jarlais and Berg 1992; Choo and Klug 1994; Jamieson et Delin Ren,1 Trevor N. Collingwood,2 al. 1994; Rebar and Pabo 1994; Greisman and Pabo 1997). Edward J. Rebar,2 Alan P. Wolffe,2 Previous studies have demonstrated the utility of both and Heidi S. Camp1,3 engineered activator- and repressor-ZFPs in the regula- tion of endogenous chromosomal loci (Bartsevich and 1Department of Molecular Science and Technology, Pfizer Juliano 2000; Beerli et al. 2000; Zhang et al. 2000; Liu et Global and Research Development, Ann Arbor, Michigan al. 2001). Our goal for this study was to selectively in- 48105, USA; 2Sangamo BioSciences Inc., Pt. Richmond, hibit expression of the PPAR␥2 isoform in the adipo- California 94804, USA genic mouse 3T3-L1 cell line by utilizing engineered zinc finger repressor proteins. To determine functional differences between the two splice variants of PPAR␥ (␥1 and ␥2), we sought to se- Results and Discussion ␥ lectively repress 2 expression by targeting engineered The mouse PPAR␥ gene spans >105 kb (Zhu et al.
    [Show full text]
  • PARP13 Regulates Cellular Mrna Post-Transcriptionally and Functions As a Pro-Apoptotic Factor by Destabilizing TRAILR4 Transcript
    ARTICLE Received 4 Sep 2014 | Accepted 23 Sep 2014 | Published 10 Nov 2014 DOI: 10.1038/ncomms6362 PARP13 regulates cellular mRNA post-transcriptionally and functions as a pro-apoptotic factor by destabilizing TRAILR4 transcript Tanya Todorova1,2, Florian J. Bock2 & Paul Chang1,2 Poly(ADP-ribose) polymerase-13 (PARP13/ZAP/ZC3HAV1) is an antiviral factor, active against specific RNA viruses such as murine leukaemia virus, Sindbis virus and human immunodeficiency virus. During infection, PARP13 binds viral RNA via its four CCCH-type zinc-finger domains and targets it for degradation by recruiting cellular messenger RNA (mRNA) decay factors such as the exosome complex and XRN1. Here we show that PARP13 binds to and regulates cellular mRNAs in the absence of viral infection. Knockdown of PARP13 results in the misregulation of hundreds of transcripts. Among the most upregulated transcripts is TRAILR4 that encodes a decoy receptor for TRAIL—a pro-apoptotic cytokine that is a promising target for the therapeutic inhibition of cancers. PARP13 destabilizes TRAILR4 mRNA post-transcriptionally in an exosome-dependent manner by binding to a region in its 30 untranslated region. As a consequence, PARP13 represses TRAILR4 expression and increases cell sensitivity to TRAIL-mediated apoptosis, acting as a key regulator of the cellular response to TRAIL. 1 Department of Biology, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, USA. 2 Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, USA. Correspondence and requests for materials should be addressed to P.C. (email: [email protected]). NATURE COMMUNICATIONS | 5:5362 | DOI: 10.1038/ncomms6362 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited.
    [Show full text]