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Zareie AR, Dabral P, Verma SC. G-Quadruplexes in the Regulation of Viral Gene Expressions and Their Impacts on Controlling Infection. Pathogens 2024; 13:60. [PMID: 38251367 PMCID: PMC10819198 DOI: 10.3390/pathogens13010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures that play significant roles in regulating various biological processes, including replication, transcription, translation, and recombination. Recent studies have identified G4s in the genomes of several viruses, such as herpes viruses, hepatitis viruses, and human coronaviruses. These structures are implicated in regulating viral transcription, replication, and virion production, influencing viral infectivity and pathogenesis. G4-stabilizing ligands, like TMPyP4, PhenDC3, and BRACO19, show potential antiviral properties by targeting and stabilizing G4 structures, inhibiting essential viral life-cycle processes. This review delves into the existing literature on G4's involvement in viral regulation, emphasizing specific G4-stabilizing ligands. While progress has been made in understanding how these ligands regulate viruses, further research is needed to elucidate the mechanisms through which G4s impact viral processes. More research is necessary to develop G4-stabilizing ligands as novel antiviral agents. The increasing body of literature underscores the importance of G4s in viral biology and the development of innovative therapeutic strategies against viral infections. Despite some ligands' known regulatory effects on viruses, a deeper comprehension of the multifaceted impact of G4s on viral processes is essential. This review advocates for intensified research to unravel the intricate relationship between G4s and viral processes, paving the way for novel antiviral treatments.
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Affiliation(s)
| | | | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, 1664 N Virginia Street, Reno, NV 89557, USA; (A.R.Z.); (P.D.)
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2
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Xu Y, Komiyama M. G-Quadruplexes in Human Telomere: Structures, Properties, and Applications. Molecules 2023; 29:174. [PMID: 38202757 PMCID: PMC10780218 DOI: 10.3390/molecules29010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
G-quadruplexes, intricate four-stranded structures composed of G-tetrads formed by four guanine bases, are prevalent in both DNA and RNA. Notably, these structures play pivotal roles in human telomeres, contributing to essential cellular functions. Additionally, the existence of DNA:RNA hybrid G-quadruplexes adds a layer of complexity to their structural diversity. This review provides a comprehensive overview of recent advancements in unraveling the intricacies of DNA and RNA G-quadruplexes within human telomeres. Detailed insights into their structural features are presented, encompassing the latest developments in chemical approaches designed to probe these G-quadruplex structures. Furthermore, this review explores the applications of G-quadruplex structures in targeting human telomeres. Finally, the manuscript outlines the imminent challenges in this evolving field, setting the stage for future investigations.
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Affiliation(s)
- Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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3
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Gao C, Mohamed HI, Deng J, Umer M, Anwar N, Chen J, Wu Q, Wang Z, He Y. Effects of Molecular Crowding on the Structure, Stability, and Interaction with Ligands of G-quadruplexes. ACS OMEGA 2023; 8:14342-14348. [PMID: 37125118 PMCID: PMC10134454 DOI: 10.1021/acsomega.3c01169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
G-quadruplexes (G4s) are widely found in cells and have significant biological functions, which makes them a target for screening antitumor and antiviral drugs. Most of the previous research on G4s has been conducted mainly in diluted solutions. However, cells are filled with organelles and many biomolecules, resulting in a constant state of a crowded molecular environment. The conformation and stability of some G4s were found to change significantly in the molecularly crowded environment, and interactions with ligands were disturbed to some extent. The structure of the G4s and their biological functions are correlated, and the effect of the molecularly crowded environment on G4 conformational transitions and interactions with ligands should be considered in drug design targeting G4s. This review discusses the changes in the conformation and stability of G4s in a physiological environment. Moreover, the mechanism of action of the molecularly crowded environment affecting the G4 has been further reviewed based on previous studies. Furthermore, current challenges and future research directions are put forward. This review has implications for the design of drugs targeting G4s.
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Affiliation(s)
- Chao Gao
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Hany I. Mohamed
- Chemistry
Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Jieya Deng
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Muhammad Umer
- Institute
for Forest Resources and Environment of Guizhou and Forestry College,
Research Center of Forest Ecology, Guizhou
University, Guiyang 550025, China
| | - Naureen Anwar
- Department
of Zoology, University of Narowal, Narowal, Punjab 51600, Pakistan
| | - Jixin Chen
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qiao Wu
- Wuhan
Botanical Garden, Chinese Academy of Science, Wuhan 430074, China
| | - Zhangqian Wang
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yi He
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
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4
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Amrane S, Jaubert C, Bedrat A, Rundstadler T, Recordon-Pinson P, Aknin C, Guédin A, De Rache A, Bartolucci L, Diene I, Lemoine F, Gascuel O, Pratviel G, Mergny JL, Andreola ML. Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection. Nucleic Acids Res 2022; 50:12328-12343. [PMID: 36453997 PMCID: PMC9757044 DOI: 10.1093/nar/gkac1030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 09/27/2022] [Accepted: 10/29/2022] [Indexed: 12/02/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures formed by the stacking of G-tetrads. Here we investigated their formation and function during HIV-1 infection. Using bioinformatics and biophysics analyses we first searched for evolutionary conserved G4-forming sequences in HIV-1 genome. We identified 10 G4s with conservation rates higher than those of HIV-1 regulatory sequences such as RRE and TAR. We then used porphyrin-based G4-binders to probe the formation of the G4s during infection of human cells by native HIV-1. The G4-binders efficiently inhibited HIV-1 infectivity, which is attributed to the formation of G4 structures during HIV-1 replication. Using a qRT-PCR approach, we showed that the formation of viral G4s occurs during the first 2 h post-infection and their stabilization by the G4-binders prevents initiation of reverse transcription. We also used a G4-RNA pull-down approach, based on a G4-specific biotinylated probe, to allow the direct detection and identification of viral G4-RNA in infected cells. Most of the detected G4-RNAs contain crucial regulatory elements such as the PPT and cPPT sequences as well as the U3 region. Hence, these G4s would function in the early stages of infection when the viral RNA genome is being processed for the reverse transcription step.
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Affiliation(s)
- Samir Amrane
- To whom correspondence should be addressed. Tel : +33 5 4000 2224;
| | - Chloé Jaubert
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Amina Bedrat
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Tiffany Rundstadler
- Université de Toulouse, UPS, INPT, Toulouse, France,Laboratoire de Chimie de Coordination, CNRS UPR 8241, Toulouse, France
| | | | - Cindy Aknin
- Université de Bordeaux, Bordeaux, France,MFP laboratory, UMR5234, CNRS, Bordeaux, France
| | - Aurore Guédin
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Aurore De Rache
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Laura Bartolucci
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Ibra Diene
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Frédéric Lemoine
- Institut Pasteur, Université de Paris, Unité de Bioinformatique Évolutive, F-75015 Paris, France,Institut Pasteur, Université de Paris, Hub de bioinformatique et biostatistiques, F-75015 Paris, France
| | - Olivier Gascuel
- Institut Pasteur, Université de Paris, Unité de Bioinformatique Évolutive, F-75015 Paris, France,Institut de Systématique, Évolution, Biodiversité (ISYEB, UMR 7205 - CNRS, Muséum National d’Histoire Naturelle, SU, EPHE UA), F-75005 Paris, France
| | - Geneviève Pratviel
- Université de Toulouse, UPS, INPT, Toulouse, France,Laboratoire de Chimie de Coordination, CNRS UPR 8241, Toulouse, France
| | - Jean-Louis Mergny
- Université de Bordeaux, Bordeaux, France,ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France,Laboratoire d’Optique & Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France
| | - Marie-Line Andreola
- Université de Bordeaux, Bordeaux, France,MFP laboratory, UMR5234, CNRS, Bordeaux, France
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5
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Zhai LY, Liu JF, Zhao JJ, Su AM, Xi XG, Hou XM. Targeting the RNA G-Quadruplex and Protein Interactome for Antiviral Therapy. J Med Chem 2022; 65:10161-10182. [PMID: 35862260 DOI: 10.1021/acs.jmedchem.2c00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, G-quadruplexes (G4s), types of noncanonical four-stranded nucleic acid structures, have been identified in many viruses that threaten human health, such as HIV and Epstein-Barr virus. In this context, G4 ligands were designed to target the G4 structures, among which some have shown promising antiviral effects. In this Perspective, we first summarize the diversified roles of RNA G4s in different viruses. Next, we introduce small-molecule ligands developed as G4 modulators and highlight their applications in antiviral studies. In addition to G4s, we comprehensively review the medical intervention of G4-interacting proteins from both the virus (N protein, viral-encoded helicases, severe acute respiratory syndrome-unique domain, and Epstein-Barr nuclear antigen 1) and the host (heterogeneous nuclear ribonucleoproteins, RNA helicases, zinc-finger cellular nucelic acid-binding protein, and nucleolin) by inhibitors as an alternative way to disturb the normal functions of G4s. Finally, we discuss the challenges and opportunities in G4-based antiviral therapy.
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Affiliation(s)
- Li-Yan Zhai
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jing-Fan Liu
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jian-Jin Zhao
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Ai-Min Su
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China.,Laboratory of Biology and Applied Pharmacology, CNRS UMR 8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
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6
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Xu J, Huang H, Zhou X. G-Quadruplexes in Neurobiology and Virology: Functional Roles and Potential Therapeutic Approaches. JACS AU 2021; 1:2146-2161. [PMID: 34977886 PMCID: PMC8715485 DOI: 10.1021/jacsau.1c00451] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 05/11/2023]
Abstract
A G-quadruplex (G4) is a four-stranded nucleic acid secondary structure maintained by Hoogsteen hydrogen bonds established between four guanines. Experimental studies and bioinformatics predictions support the hypothesis that these structures are involved in different cellular functions associated with both DNA and RNA processes. An increasing number of diseases have been shown to be associated with abnormal G4 regulation. Here, we describe the existence of G4 and then discuss G4-related pathogenic mechanisms in neurodegenerative diseases and the viral life cycle. Furthermore, we focus on the role of G4s in the design of antiviral therapy and neuropharmacology, including G4 ligands, G4-based aptamers, G4-related proteins, and CRISPR-based sequence editing, along with a discussion of limitations and insights into the prospects of this unusual nucleic acid secondary structure in therapeutics. Finally, we highlight progress and challenges in this field and the potential G4-related research fields.
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Affiliation(s)
- Jinglei Xu
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
| | - Haiyan Huang
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Xiang Zhou
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
- Email to X.Z.:
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7
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Zheng AJL, Thermou A, Guixens Gallardo P, Malbert-Colas L, Daskalogianni C, Vaudiau N, Brohagen P, Granzhan A, Blondel M, Teulade-Fichou MP, Martins RP, Fahraeus R. The different activities of RNA G-quadruplex structures are controlled by flanking sequences. Life Sci Alliance 2021; 5:5/2/e202101232. [PMID: 34785537 PMCID: PMC8605322 DOI: 10.26508/lsa.202101232] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/17/2022] Open
Abstract
The role of G-quadruplex (G4) RNA structures is multifaceted and controversial. Here, we have used as a model the EBV-encoded EBNA1 and the Kaposi's sarcoma-associated herpesvirus (KSHV)-encoded LANA1 mRNAs. We have compared the G4s in these two messages in terms of nucleolin binding, nuclear mRNA retention, and mRNA translation inhibition and their effects on immune evasion. The G4s in the EBNA1 message are clustered in one repeat sequence and the G4 ligand PhenDH2 prevents all G4-associated activities. The RNA G4s in the LANA1 message take part in similar multiple mRNA functions but are spread throughout the message. The different G4 activities depend on flanking coding and non-coding sequences and, interestingly, can be separated individually. Together, the results illustrate the multifunctional, dynamic and context-dependent nature of G4 RNAs and highlight the possibility to develop ligands targeting specific RNA G4 functions. The data also suggest a common multifunctional repertoire of viral G4 RNA activities for immune evasion.
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Affiliation(s)
- Alice J-L Zheng
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France
| | - Aikaterini Thermou
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France.,ICCVS, University of Gdańsk, Science, Gdańsk, Poland
| | - Pedro Guixens Gallardo
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Laurence Malbert-Colas
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France
| | - Chrysoula Daskalogianni
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France.,ICCVS, University of Gdańsk, Science, Gdańsk, Poland
| | - Nathan Vaudiau
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France
| | - Petter Brohagen
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Marc Blondel
- Inserm UMR1078, Université de Bretagne Occidentale (UBO), Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Brest, France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | | | - Robin Fahraeus
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France .,RECAMO, Masaryk Memorial Cancer Institute, Brno, Czech Republic.,Department of Medical Biosciences, Umeå University, Umeå, Sweden.,ICCVS, University of Gdańsk, Science, Gdańsk, Poland
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8
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Gold(III) porphyrins: Synthesis and interaction with G-quadruplex DNA. J Inorg Biochem 2021; 223:111551. [PMID: 34340058 DOI: 10.1016/j.jinorgbio.2021.111551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/09/2021] [Accepted: 07/15/2021] [Indexed: 12/25/2022]
Abstract
G-quadruplex nucleic acids (G4s) are RNA and DNA secondary structures involved in the regulation of multiple key biological processes. They can be found in telomeres, oncogene promoters, RNAs, but also in viral genomes. Due to their unique structural features, very distinct from the canonical duplexes or single-strands, G4s represent promising pharmacological targets for small molecules, namely G4-ligands. Gold(III) penta-cationic porphyrins, as specific G4 ligands, are able to inhibit HIV-1 infectivity and their antiviral activity correlates with their affinity for G4s. Up to now, one of the best antiviral compounds is meso-5,10,15,20-tetrakis[4-(N-methyl-pyridinium-2-yl)phenyl]porphyrinato gold(III) (1). Starting from this compound, we report a structure/affinity relationship study of gold(III) cationic porphyrins to find out the best porphyrin candidate for functionalization, in order to study the antiviral mechanism of action of these gold(III) porphyrins.
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9
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Abiri A, Lavigne M, Rezaei M, Nikzad S, Zare P, Mergny JL, Rahimi HR. Unlocking G-Quadruplexes as Antiviral Targets. Pharmacol Rev 2021; 73:897-923. [PMID: 34045305 DOI: 10.1124/pharmrev.120.000230] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Guanine-rich DNA and RNA sequences can fold into noncanonical nucleic acid structures called G-quadruplexes (G4s). Since the discovery that these structures may act as scaffolds for the binding of specific ligands, G4s aroused the attention of a growing number of scientists. The versatile roles of G4 structures in viral replication, transcription, and translation suggest direct applications in therapy or diagnostics. G4-interacting molecules (proteins or small molecules) may also affect the balance between latent and lytic phases, and increasing evidence reveals that G4s are implicated in generally suppressing viral processes, such as replication, transcription, translation, or reverse transcription. In this review, we focus on the discovery of G4s in viruses and the role of G4 ligands in the antiviral drug discovery process. After assessing the role of viral G4s, we argue that host G4s participate in immune modulation, viral tumorigenesis, cellular pathways involved in virus maturation, and DNA integration of viral genomes, which can be potentially employed for antiviral therapeutics. Furthermore, we scrutinize the impediments and shortcomings in the process of studying G4 ligands and drug discovery. Finally, some unanswered questions regarding viral G4s are highlighted for prospective future projects. SIGNIFICANCE STATEMENT: G-quadruplexes (G4s) are noncanonical nucleic acid structures that have gained increasing recognition during the last few decades. First identified as relevant targets in oncology, their importance in virology is now increasingly clear. A number of G-quadruplex ligands are known: viral transcription and replication are the main targets of these ligands. Both viral and cellular G4s may be targeted; this review embraces the different aspects of G-quadruplexes in both host and viral contexts.
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Affiliation(s)
- Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Marc Lavigne
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Masoud Rezaei
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Sanaz Nikzad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Peyman Zare
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Jean-Louis Mergny
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Hamid-Reza Rahimi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
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10
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Harpster C, Boyle E, Musier-Forsyth K, Kankia B. HIV-1 genomic RNA U3 region forms a stable quadruplex-hairpin structure. Biophys Chem 2021; 272:106567. [PMID: 33713997 PMCID: PMC8051326 DOI: 10.1016/j.bpc.2021.106567] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/22/2021] [Accepted: 02/28/2021] [Indexed: 01/14/2023]
Abstract
The U3 promoter region of the HIV-1 long terminal repeat (LTR) has previously been shown to fold into a series of dynamic G-quadruplex structures. Among the G-quadruplexes identified in the LTR sequence, LTR-III was shown to be the most stable in vitro. NMR studies of this 28-nucleotide (nt) DNA revealed a unique quadruplex-hairpin structure. Whether the hairpin forms in RNA element is unknown and the role of the hairpin in the structure and stability of quadruplexes has not been characterized. Here, we used optical and thermodynamic studies to address these questions. The wild-type LTR-III RNA formed a monomolecular quadruplex with a parallel topology using only propeller loops, including the hairpin loop element. By comparison to the WT and variant RNAs, LTR-III DNA structures were more heterogeneous and less stable. Increased stability of the RNA suggests that the RNA quadruplex-hairpin structure may be a more attractive therapeutic target than the analogous DNA element.
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Affiliation(s)
- Chelsea Harpster
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Elaina Boyle
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Besik Kankia
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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11
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Ruggiero E, Richter SN. Viral G-quadruplexes: New frontiers in virus pathogenesis and antiviral therapy. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2020; 54:101-131. [PMID: 32427223 PMCID: PMC7233243 DOI: 10.1016/bs.armc.2020.04.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Viruses are the most abundant organisms on our planet, affecting all living beings: some of them are responsible for massive epidemics that concern health, national economies and the overall welfare of societies. Although advances in antiviral research have led to successful therapies against several human viruses, still some of them cannot be eradicated from the host and most of them do not have any treatment available. Consequently, innovative antiviral therapies are urgently needed. In the past few years, research on G-quadruplexes (G4s) in viruses has boomed, providing powerful evidence for the regulatory role of G4s in key viral steps. Comprehensive bioinformatics analyses have traced putative G4-forming sequences in the genome of almost all human viruses, showing that their distribution is statistically significant and their presence highly conserved. Since the genomes of viruses are remarkably variable, high conservation rates strongly suggest a crucial role of G4s in the viral replication cycle and evolution, emphasizing the possibility of targeting viral G4s as a new pharmacological approach in antiviral therapy. Recent studies have demonstrated the formation and function of G4s in pathogens responsible for serious diseases, such as HIV-1, Hepatitis B and C, Ebola viruses, to cite a few. In this chapter, we present the state of the art on the structural and functional characterization of viral G4s in RNA viruses, DNA viruses and retroviruses. We also present the G4 ligands that provide further details on the viral G4 role and which, showing promising antiviral activity, which could be exploited for the development of innovative antiviral agents.
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Affiliation(s)
| | - Sara N. Richter
- Department of Molecular Medicine, University of Padua, Padua, Italy
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12
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LANA and hnRNP A1 Regulate the Translation of LANA mRNA through G-Quadruplexes. J Virol 2020; 94:JVI.01508-19. [PMID: 31723020 DOI: 10.1128/jvi.01508-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/04/2019] [Indexed: 12/26/2022] Open
Abstract
During the latent phase, Kaposi's sarcoma-associated herpes virus (KSHV) maintains itself inside the host by escaping the host immune surveillance mechanism through restricted protein expression. Latency-associated nuclear antigen (LANA), the most abundantly expressed protein, is essential for viral persistence, as it plays important roles in latent viral DNA replication and efficient segregation of the viral genome to the daughter cells following cell division. KSHV evades immune detection by maintaining the levels of LANA protein below a threshold required for detection by the host immune system but sufficient to maintain the viral genome. LANA achieves this by controlling its expression through regulation of its promoters and by inhibiting its presentation through interaction with the proteins of class I and class II major histocompatibility complex (MHC) pathways. In this study, we identified a mechanism of LANA expression and restricted immune recognition through formation of G-quadruplexes in LANA mRNA. We show that the formation of these stable structures in LANA mRNA inhibits its translation to control antigen presentation, which was supported by treatment of cells with TMPyP4, a G-quadruplex-stabilizing ligand. We identified heterogenous ribonucleoprotein A1 (hnRNP A1) as a G-quadruplex-unwinding helicase, which unfolds these stable secondary structures to regulate LANA translation.IMPORTANCE LANA, the most abundantly expressed protein during latency, is a multifunctional protein which is absolutely required for the persistence of KSHV in the host cell. Even though the functions of LANA in aiding pathogenesis of the virus have been extensively studied, the mechanism of how LANA escapes host's immune surveillance is not fully understood. This study sheds light on the autoregulatory role of LANA to modulate its expression and immune evasion through formation of G-quadruplexes in its mRNA. We used G-quadruplex-stabilizing ligand to define the inhibition in LANA expression and presentation on the cell surface through MHC class I. We defined the autoregulatory role of LANA and identified a cellular RNA helicase, hnRNP A1, regulating the translation of LANA mRNA. This interaction of hnRNP A1 with LANA mRNA could be exploited for controlling KSHV latency.
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13
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Skittrall JP, Ingemarsdotter CK, Gog JR, Lever AML. A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance. PLoS Comput Biol 2019; 15:e1007345. [PMID: 31545786 PMCID: PMC6791557 DOI: 10.1371/journal.pcbi.1007345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/14/2019] [Accepted: 08/19/2019] [Indexed: 12/22/2022] Open
Abstract
HIV-1 replicates via a low-fidelity polymerase with a high mutation rate; strong conservation of individual nucleotides is highly indicative of the presence of critical structural or functional properties. Identifying such conservation can reveal novel insights into viral behaviour. We analysed 3651 publicly available sequences for the presence of nucleic acid conservation beyond that required by amino acid constraints, using a novel scale-free method that identifies regions of outlying score together with a codon scoring algorithm. Sequences with outlying score were further analysed using an algorithm for producing local RNA folds whilst accounting for alignment properties. 11 different conserved regions were identified, some corresponding to well-known cis-acting functions of the HIV-1 genome but also others whose conservation has not previously been noted. We identify rational causes for many of these, including cis functions, possible additional reading frame usage, a plausible mechanism by which the central polypurine tract primes second-strand DNA synthesis and a conformational stabilising function of a region at the 5′ end of env. HIV-1 is a very rapidly mutating organism, however some parts of its genetic material change more than others. We looked for coding regions of HIV-1 that change relatively little, by turning the problem of finding such regions into a problem in signal processing, and solving this using a novel analytical approach that we recently described. We investigated why the regions we identified change less, including using the genetic code in the regions we found to prime an algorithm to predict their structures. In some cases there are already known functions for the features we found, in others they provide new insights into the properties of known regions, and in some cases we identify new regions that vary less for as yet unknown functional reasons.
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Affiliation(s)
- Jordan P Skittrall
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Carin K Ingemarsdotter
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Julia R Gog
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Centre for Mathematical Sciences, Cambridge, United Kingdom
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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14
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Kharel P, Balaratnam S, Beals N, Basu S. The role of RNA G-quadruplexes in human diseases and therapeutic strategies. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1568. [PMID: 31514263 DOI: 10.1002/wrna.1568] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 08/09/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022]
Abstract
G-quadruplexes (GQs) are four-stranded secondary structures formed by G-rich nucleic acid sequence(s). DNA GQs are present abundantly in the genome and affect a wide range of processes associated with DNA. Recent studies show that RNA GQs are present in different transcripts, including coding and noncoding areas of mRNA, telomeric RNA as well as in other premature and mature noncoding RNAs. When present at specific locations within the RNAs, GQs play important roles in key biological functions, including the regulation of gene expression and telomere homeostasis. RNA GQs regulate pre-mRNA processing, such as splicing and polyadenylation. Evidently, among other processes, RNA GQs also control mRNA translation, miRNA and piRNA biogenesis, and RNA localization. The regulatory mechanisms controlled by RNA GQs mainly involve binding to RNA binding protein that modulate GQ conformation or serve as an entity in recruiting additional protein regulators to act as a block element to the processing machinery. Here we provide an overview of the ever-increasing number of discoveries revealing the role of RNA GQs in biology and their relevance in human diseases and therapeutics. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Prakash Kharel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio.,Division of Rheumatology, Immunology, and Allergy, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sumirtha Balaratnam
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio.,Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland
| | - Nathan Beals
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio
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15
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Ruggiero E, Richter SN. G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy. Nucleic Acids Res 2019; 46:3270-3283. [PMID: 29554280 PMCID: PMC5909458 DOI: 10.1093/nar/gky187] [Citation(s) in RCA: 270] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/02/2018] [Indexed: 12/13/2022] Open
Abstract
G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that form within guanine-rich strands of regulatory genomic regions. G4s have been extensively described in the human genome, especially in telomeres and oncogene promoters; in recent years the presence of G4s in viruses has attracted increasing interest. Indeed, G4s have been reported in several viruses, including those involved in recent epidemics, such as the Zika and Ebola viruses. Viral G4s are usually located in regulatory regions of the genome and implicated in the control of key viral processes; in some cases, they have been involved also in viral latency. In this context, G4 ligands have been developed and tested both as tools to study the complexity of G4-mediated mechanisms in the viral life cycle, and as therapeutic agents. In general, G4 ligands showed promising antiviral activity, with G4-mediated mechanisms of action both at the genome and transcript level. This review aims to provide an updated close-up of the literature on G4s in viruses. The current state of the art of G4 ligands in antiviral research is also reported, with particular focus on the structural and physicochemical requirements for optimal biological activity. The achievements and the to-dos in the field are discussed.
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Affiliation(s)
- Emanuela Ruggiero
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
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16
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Saranathan N, Biswas B, Patra A, Vivekanandan P. G-quadruplexes may determine the landscape of recombination in HSV-1. BMC Genomics 2019; 20:382. [PMID: 31096907 PMCID: PMC6524338 DOI: 10.1186/s12864-019-5731-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
Background Several lines of evidence suggest that recombination plays a central role in replication and evolution of herpes simplex virus-1 (HSV-1). G-quadruplex (G4)-motifs have been linked to recombination events in human and microbial genomes, but their role in recombination has not been studied in DNA viruses. Results The availability of near full-length sequences from 40 HSV-1 recombinant strains with exact position of the recombination breakpoints provided us with a unique opportunity to investigate the role of G4-motifs in recombination among herpes viruses. We mapped the G4-motifs in the parental and all the 40 recombinant strains. Interestingly, the genome-wide distribution of breakpoints closely mirrors the G4 densities in the HSV-1 genome; regions of the genome with higher G4 densities had higher number of recombination breakpoints. Biophysical characterization of oligonucleotides from a subset of predicted G4-motifs confirmed the formation of G-quadruplex structures. Our analysis also reveals that G4-motifs are enriched in regions flanking the recombination breakpoints. Interestingly, about 11% of breakpoints lie within a G4-motif, making these DNA secondary structures hotspots for recombination in the HSV-1 genome. Breakpoints within G4-motifs predominantly lie within G4-clusters rather than individual G4-motifs. Of note, we identified the terminal guanosine of G4-clusters at the boundaries of the UL (unique long) region on either side of the OriL (origin of replication within UL) represented the commonest breakpoint among the HSV-1 recombinants. Conclusion Our findings suggest a correlation between the HSV-1 recombination landscape and the distribution of G4-motifs and G4-clusters, with possible implications for the evolution of DNA viruses. Electronic supplementary material The online version of this article (10.1186/s12864-019-5731-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nandhini Saranathan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Banhi Biswas
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Anupam Patra
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.
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17
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Fleming AM, Nguyen NLB, Burrows CJ. Colocalization of m 6A and G-Quadruplex-Forming Sequences in Viral RNA (HIV, Zika, Hepatitis B, and SV40) Suggests Topological Control of Adenosine N 6-Methylation. ACS CENTRAL SCIENCE 2019; 5:218-228. [PMID: 30834310 PMCID: PMC6396389 DOI: 10.1021/acscentsci.8b00963] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Indexed: 05/09/2023]
Abstract
This Outlook calls attention to two seemingly disparate and emerging fields regarding viral genomics that may be correlated in a way previously overlooked. First, we describe identification of conserved potential G-quadruplex-forming sequences (PQSs) in viral genomes relevant to human health. Studies have demonstrated that PQSs are highly conserved and can fold to G-quadruplexes (G4s) to regulate viral processes. Key examples include G4s as a countermeasure to the host's immune system or G4-guided regulation of replication or transcription. Second, emerging data are discussed concerning the epitranscriptomic modification N 6-methyladenosine (m6A) in viral RNA installed by host proteins in a consensus sequence favoring 5'-GG(m6A)C-3'. The proposed pathways by which m6A is written, read, and erased in viral RNA genomes and the impact this has on viral replication are described. The structural reason why certain sites are selected for modification while others are not is still mysterious. Finally, we discuss our new observations regarding these previous sequencing data that identify m6A installation within the loops of two-tetrad PQSs in the RNA genomes of the Zika, HIV, hepatitis B, and SV40 viruses. We hypothesize that conserved viral PQSs can provide a framework (sequence and/or structural) for m6A installation. We also discuss literature sources suggesting that PQSs as sites of RNA modification could be a general phenomenon. We anticipate our observations will provide ample opportunities for exciting discoveries regarding the interplay between G4 structures and epitranscriptomic modifications of RNA.
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Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry, University
of Utah, Salt Lake
City, Utah 84112-0850, United States
| | - Ngoc L. B. Nguyen
- Department of Chemistry, University
of Utah, Salt Lake
City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University
of Utah, Salt Lake
City, Utah 84112-0850, United States
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18
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Saranathan N, Vivekanandan P. G-Quadruplexes: More Than Just a Kink in Microbial Genomes. Trends Microbiol 2019; 27:148-163. [PMID: 30224157 PMCID: PMC7127049 DOI: 10.1016/j.tim.2018.08.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/17/2018] [Accepted: 08/24/2018] [Indexed: 02/06/2023]
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid secondary structures formed by guanine-rich DNA and RNA sequences. In this review we aim to provide an overview of the biological roles of G4s in microbial genomes with emphasis on recent discoveries. G4s are enriched and conserved in the regulatory regions of microbes, including bacteria, fungi, and viruses. Importantly, G4s in hepatitis B virus (HBV) and hepatitis C virus (HCV) genomes modulate genes crucial for virus replication. Recent studies on Epstein-Barr virus (EBV) shed light on the role of G4s within the microbial transcripts as cis-acting regulatory signals that modulate translation and facilitate immune evasion. Furthermore, G4s in microbial genomes have been linked to radioresistance, antigenic variation, recombination, and latency. G4s in microbial genomes represent novel therapeutic targets for antimicrobial therapy.
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Affiliation(s)
- Nandhini Saranathan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.
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19
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Tokan V, Puterova J, Lexa M, Kejnovsky E. Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast. BMC Genomics 2018; 19:184. [PMID: 29510672 PMCID: PMC5838962 DOI: 10.1186/s12864-018-4563-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/20/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Many studies have shown that guanine-rich DNA sequences form quadruplex structures (G4) in vitro but there is scarce evidence of guanine quadruplexes in vivo. The majority of potential quadruplex-forming sequences (PQS) are located in transposable elements (TEs), especially close to promoters within long terminal repeats of plant LTR retrotransposons. RESULTS In order to test the potential effect of G4s on retrotransposon expression, we cloned the long terminal repeats of selected maize LTR retrotransposons upstream of the lacZ reporter gene and measured its transcription and translation in yeast. We found that G4s had an inhibitory effect on translation in vivo since "mutants" (where guanines were replaced by adenines in PQS) showed higher expression levels than wild-types. In parallel, we confirmed by circular dichroism measurements that the selected sequences can indeed adopt G4 conformation in vitro. Analysis of RNA-Seq of polyA RNA in maize seedlings grown in the presence of a G4-stabilizing ligand (NMM) showed both inhibitory as well as stimulatory effects on the transcription of LTR retrotransposons. CONCLUSIONS Our results demonstrate that quadruplex DNA located within long terminal repeats of LTR retrotransposons can be formed in vivo and that it plays a regulatory role in the LTR retrotransposon life-cycle, thus also affecting genome dynamics.
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Affiliation(s)
- Viktor Tokan
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic
| | - Janka Puterova
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 61200 Brno, Czech Republic
| | - Matej Lexa
- Faculty of Informatics, Masaryk University, Botanicka 68a, 60200 Brno, Czech Republic
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic
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20
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Putative HIV and SIV G-Quadruplex Sequences in Coding and Noncoding Regions Can Form G-Quadruplexes. J Nucleic Acids 2017; 2017:6513720. [PMID: 29464116 PMCID: PMC5804116 DOI: 10.1155/2017/6513720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/26/2017] [Accepted: 10/18/2017] [Indexed: 11/17/2022] Open
Abstract
The HIV virus is one of the most studied viruses in the world. This is especially true in terms of gene sequencing, and to date more than 9 thousand genomic sequences of HIV isolates have been sequenced and analyzed. In this study, a series of DNA sequences, which have the potential to form G-quadruplex structures, is analyzed. Several such sequences were found in various coding and noncoding virus domains, including the U3 LTR, tat, rev, env, and vpx regions. Interestingly, a homological sequence to the already well-known HIV integrase aptamer was identified in the minus-strand. The sequences derived from original isolates were analyzed using standard spectral and electrophoretic methods. In addition, a recently developed methodology is applied which uses induced circular dichroism spectral profiles of G-quadruplex-ligand (Thiazole Orange) complexes to determine if G-rich sequences can adopt G-quadruplex structure. Targeting the G-quadruplexes or peptide domains corresponding to the G-rich coding sequence in HIV offers researchers attractive therapeutic targets which would be of particular use in the development of novel antiviral therapies. The analysis of G-rich regions can provide researchers with a path to find specific targets which could be of interest for specific types of virus.
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21
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Piekna-Przybylska D, Sharma G, Maggirwar SB, Bambara RA. Deficiency in DNA damage response, a new characteristic of cells infected with latent HIV-1. Cell Cycle 2017; 16:968-978. [PMID: 28388353 DOI: 10.1080/15384101.2017.1312225] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Viruses can interact with host cell molecules responsible for the recognition and repair of DNA lesions, resulting in dysfunctional DNA damage response (DDR). Cells with inefficient DDR are more vulnerable to therapeutic approaches that target DDR, thereby raising DNA damage to a threshold that triggers apoptosis. Here, we demonstrate that 2 Jurkat-derived cell lines with incorporated silent HIV-1 provirus show increases in DDR signaling that responds to formation of double strand DNA breaks (DSBs). We found that phosphorylation of histone H2AX on Ser139 (gamma-H2AX), a biomarker of DSBs, and phosphorylation of ATM at Ser1981, Chk2 at Thr68, and p53 at Ser15, part of signaling pathways associated with DSBs, are elevated in these cells. These results indicate a DDR defect even though the virus is latent. DDR-inducing agents, specifically high doses of nucleoside RT inhibitors (NRTIs), caused greater increases in gamma-H2AX levels in latently infected cells. Additionally, latently infected cells are more susceptible to long-term exposure to G-quadruplex stabilizing agents, and this effect is enhanced when the agent is combined with an inhibitor targeting DNA-PK, which is crucial for DSB repair and telomere maintenance. Moreover, exposing these cells to the cancer drug etoposide resulted in formation of DSBs at a higher rate than in un-infected cells. Similar effects of etoposide were also observed in population of primary memory T cells infected with latent HIV-1. Sensitivity to these agents highlights a unique vulnerability of latently infected cells, a new feature that could potentially be used in developing therapies to eliminate HIV-1 reservoirs.
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Affiliation(s)
- Dorota Piekna-Przybylska
- a Department of Microbiology and Immunology , School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
| | - Gaurav Sharma
- b Department of Electrical and Computer Engineering , University of Rochester , Rochester , NY , USA
| | - Sanjay B Maggirwar
- a Department of Microbiology and Immunology , School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
| | - Robert A Bambara
- a Department of Microbiology and Immunology , School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
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22
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Menéndez-Arias L, Sebastián-Martín A, Álvarez M. Viral reverse transcriptases. Virus Res 2016; 234:153-176. [PMID: 28043823 DOI: 10.1016/j.virusres.2016.12.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/19/2016] [Accepted: 12/24/2016] [Indexed: 12/11/2022]
Abstract
Reverse transcriptases (RTs) play a major role in the replication of Retroviridae, Metaviridae, Pseudoviridae, Hepadnaviridae and Caulimoviridae. RTs are enzymes that are able to synthesize DNA using RNA or DNA as templates (DNA polymerase activity), and degrade RNA when forming RNA/DNA hybrids (ribonuclease H activity). In retroviruses and LTR retrotransposons (Metaviridae and Pseudoviridae), the coordinated action of both enzymatic activities converts single-stranded RNA into a double-stranded DNA that is flanked by identical sequences known as long terminal repeats (LTRs). RTs of retroviruses and LTR retrotransposons are active as monomers (e.g. murine leukemia virus RT), homodimers (e.g. Ty3 RT) or heterodimers (e.g. human immunodeficiency virus type 1 (HIV-1) RT). RTs lack proofreading activity and display high intrinsic error rates. Besides, high recombination rates observed in retroviruses are promoted by poor processivity that causes template switching, a hallmark of reverse transcription. HIV-1 RT inhibitors acting on its polymerase activity constitute the backbone of current antiretroviral therapies, although novel drugs, including ribonuclease H inhibitors, are still necessary to fight HIV infections. In Hepadnaviridae and Caulimoviridae, reverse transcription leads to the formation of nicked circular DNAs that will be converted into episomal DNA in the host cell nucleus. Structural and biochemical information on their polymerases is limited, although several drugs inhibiting HIV-1 RT are known to be effective against the human hepatitis B virus polymerase. In this review, we summarize current knowledge on reverse transcription in the five virus families and discuss available biochemical and structural information on RTs, including their biosynthesis, enzymatic activities, and potential inhibition.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Alba Sebastián-Martín
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Mar Álvarez
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain
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23
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Krafčíková P, Demkovičová E, Víglaský V. Ebola virus derived G-quadruplexes: Thiazole orange interaction. Biochim Biophys Acta Gen Subj 2016; 1861:1321-1328. [PMID: 27979676 DOI: 10.1016/j.bbagen.2016.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/05/2016] [Accepted: 12/11/2016] [Indexed: 10/20/2022]
Abstract
The Ebola and Marburg viruses are some of the deadliest viruses in the world. In this study a series of G-rich DNA sequences derived from these types of viruses which possess the potential to form G-quadruplex structures are analyzed. A set of DNA oligonucleotides derived from original viral isolates was used as a representative modeling sequence with which to demonstrate the influence of thiazole orange on circular dichroism (CD) spectral profiles. The results show the unique profile of the induced CD (ICD) signal in the visible region caused by interactions between the ligand and G-quadruplexes. This ligand was found to stabilize the G-quadruplex structure and can also induce topological changes and facilitate G-quadruplex multimerization. Thus, the ICD signatures can be used to determine whether specific unknown sequences can form G-quadruplex motifs. The viral sequences were analyzed using standard spectral and electrophoretic methods. In addition, the ability to target G-quadruplexes located in filoviruses offers researchers attractive therapeutic targets which would be of particular use in the development of novel antiviral therapies. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Petra Krafčíková
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Safarik University, 04001, Kosice, Slovakia
| | - Erika Demkovičová
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Safarik University, 04001, Kosice, Slovakia
| | - Viktor Víglaský
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Safarik University, 04001, Kosice, Slovakia.
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24
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Nikolaitchik O, Keele B, Gorelick R, Alvord WG, Mazurov D, Pathak VK, Hu WS. High recombination potential of subtype A HIV-1. Virology 2015; 484:334-340. [PMID: 26164392 PMCID: PMC6258064 DOI: 10.1016/j.virol.2015.06.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 05/28/2015] [Accepted: 06/09/2015] [Indexed: 01/18/2023]
Abstract
Recombination can assort polymorphic alleles to increase diversity in the HIV-1 population. To better understand the recombination potential of subtype A HIV-1, we generated viruses containing sequences from two variants circulating in Russia and analyzed the polymerase gene (pol) of the recombinants after one round of HIV-1 replication using single-genome sequencing. We observed that recombination occurred throughout pol and could easily assort alleles containing mutations that conferred resistance to currently approved antivirals. We measured the recombination rate in various regions of pol including a G-rich region that has been previously proposed to be a recombination hot spot. Our study does not support a recombination hot spot in this G-rich region. Importantly, of the 58 proviral sequences containing crossover event(s) in pol, we found that each sequence was a unique genotype indicating that recombination is a powerful genetic mechanism in assorting the genomes of subtype A HIV-1 variants.
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Affiliation(s)
- Olga Nikolaitchik
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Brandon Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - W Gregory Alvord
- Data Management Services, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Dmitriy Mazurov
- Institute of Immunology, Kashirskoe shosse 24-2, Moscow 115478, Russia
| | - Vinay K Pathak
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Wei-Shau Hu
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA.
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Abstract
DNA can form several secondary structures besides the classic double helix: one that has received much attention in recent years is the G-quadruplex (G4). This is a stable four-stranded structure formed by the stacking of quartets of guanine bases. Recent work has convincingly shown that G4s can form in vivo as well as in vitro and can affect both replication and transcription of DNA. They also play important roles at G-rich telomeres. Now, a spate of exciting reports has begun to reveal roles for G4 structures in virulence processes in several important microbial pathogens of humans. Interestingly, these come from a range of kingdoms—bacteria and protozoa as well as viruses—and all facilitate immune evasion in different ways. In particular, roles for G4s have been posited in the antigenic variation systems of bacteria and protozoa, as well as in the silencing of at least two major human viruses, human immunodeficiency virus (HIV) and Epstein-Barr virus (EBV). Although antigenic variation and the silencing of latent viruses are quite distinct from one another, both are routes to immune evasion and the maintenance of chronic infections. Thus, highly disparate pathogens can use G4 motifs to control DNA/RNA dynamics in ways that are relevant to common virulence phenotypes. This review explores the evidence for G4 biology in such processes across a range of important human pathogens.
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26
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Métifiot M, Amrane S, Litvak S, Andreola ML. G-quadruplexes in viruses: function and potential therapeutic applications. Nucleic Acids Res 2014; 42:12352-66. [PMID: 25332402 PMCID: PMC4227801 DOI: 10.1093/nar/gku999] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/26/2014] [Accepted: 10/06/2014] [Indexed: 12/15/2022] Open
Abstract
G-rich nucleic acids can form non-canonical G-quadruplex structures (G4s) in which four guanines fold in a planar arrangement through Hoogsteen hydrogen bonds. Although many biochemical and structural studies have focused on DNA sequences containing successive, adjacent guanines that spontaneously fold into G4s, evidence for their in vivo relevance has recently begun to accumulate. Complete sequencing of the human genome highlighted the presence of ∼300,000 sequences that can potentially form G4s. Likewise, the presence of putative G4-sequences has been reported in various viruses genomes [e.g., Human immunodeficiency virus (HIV-1), Epstein-Barr virus (EBV), papillomavirus (HPV)]. Many studies have focused on telomeric G4s and how their dynamics are regulated to enable telomere synthesis. Moreover, a role for G4s has been proposed in cellular and viral replication, recombination and gene expression control. In parallel, DNA aptamers that form G4s have been described as inhibitors and diagnostic tools to detect viruses [e.g., hepatitis A virus (HAV), EBV, cauliflower mosaic virus (CaMV), severe acute respiratory syndrome virus (SARS), simian virus 40 (SV40)]. Here, special emphasis will be given to the possible role of these structures in a virus life cycle as well as the use of G4-forming oligonucleotides as potential antiviral agents and innovative tools.
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Affiliation(s)
- Mathieu Métifiot
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Samir Amrane
- INSERM, U869, IECB, ARNA laboratory, Université de Bordeaux, 2 Rue Robert Escarpit 33600 Pessac, France
| | - Simon Litvak
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Marie-Line Andreola
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
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Perrone R, Butovskaya E, Daelemans D, Palù G, Pannecouque C, Richter SN. Anti-HIV-1 activity of the G-quadruplex ligand BRACO-19. J Antimicrob Chemother 2014; 69:3248-58. [PMID: 25103489 DOI: 10.1093/jac/dku280] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES A dynamic G-quadruplex region has been previously shown to form in the long terminal repeat (LTR) promoter of the HIV-1 integrated DNA genome. Inhibition of promoter activity and antiviral effects have been observed when this region was stabilized by BRACO-19, a trisubstituted acridine derivative that binds G-quadruplexes. Here, we aimed at characterizing the antiviral mechanism of action of BRACO-19 by analysing its activity towards a broad range of HIV-1 strains, host cells and infection modes. METHODS The antiviral activity of BRACO-19 in cell lines and primary cells infected or persistently infected by HIV-1 strains was evaluated at different times post-infection. Virucidal, viral binding, time-dependent and drug-dependent assays were performed to identify the viral target step. Circular dichroism, UV spectroscopy and a reverse transcriptase (RT) stop assay were used to assess RNA G-quadruplex folding and inhibition of RT processing. RESULTS Thorough virological assays demonstrated that BRACO-19 acts both at the reverse transcription and the post-integration level during the virus life cycle. This behaviour was rationalized by the observation that a G-quadruplex-forming sequence identical to that of the LTR DNA is present at the 3'-end of the virus RNA genome. Biophysics and biomolecular testing showed that this region has the ability to fold into very stable G-quadruplex structures that are even more stabilized by BRACO-19, therefore inhibiting the reverse transcription process at the template level. CONCLUSIONS Our findings strongly support the activity of BRACO-19 at the viral G-quadruplex level and therefore strengthen the use of viral G-quadruplexes as new anti-HIV-1 targets.
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Affiliation(s)
- Rosalba Perrone
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Elena Butovskaya
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Dirk Daelemans
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Padua, Italy
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Piekna-Przybylska D, Sullivan MA, Sharma G, Bambara RA. U3 region in the HIV-1 genome adopts a G-quadruplex structure in its RNA and DNA sequence. Biochemistry 2014; 53:2581-93. [PMID: 24735378 PMCID: PMC4007979 DOI: 10.1021/bi4016692] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Genomic regions rich in G residues
are prone to adopt G-quadruplex
structure. Multiple Sp1-binding motifs arranged in tandem have been
suggested to form this structure in promoters of cancer-related genes.
Here, we demonstrate that the G-rich proviral DNA sequence of the
HIV-1 U3 region, which serves as a promoter of viral transcription,
adopts a G-quadruplex structure. The sequence contains three binding
elements for transcription factor Sp1, which is involved in the regulation
of HIV-1 latency, reactivation, and high-level virus expression. We
show that the three Sp1 binding motifs can adopt different forms of
G-quadruplex structure and that the Sp1 protein can recognize and
bind to its site folded into a G-quadruplex. In addition, a c-kit2
specific antibody, designated hf2, binds to two different G-quadruplexes
formed in Sp1 sites. Since U3 is encoded at both viral genomic ends,
the G-rich sequence is also present in the RNA genome. We demonstrate
that the RNA sequence of U3 forms dimers with characteristics known
for intermolecular G-quadruplexes. Together with previous reports
showing G-quadruplex dimers in the gag and cPPT regions,
these results suggest that integrity of the two viral genomes is maintained
through numerous intermolecular G-quadruplexes formed in different
RNA genome locations. Reconstituted reverse transcription shows that
the potassium-dependent structure formed in U3 RNA facilitates RT
template switching, suggesting that the G-quadruplex contributes to
recombination in U3.
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Affiliation(s)
- Dorota Piekna-Przybylska
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester , Rochester, New York 14642, United States
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29
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Mathias J, Okyere R, Lomidze L, Gvarjaladze D, Musier-Forsyth K, Kankia B. Thermal stability of quadruplex primers for highly versatile isothermal DNA amplification. Biophys Chem 2013; 185:14-8. [PMID: 24317195 DOI: 10.1016/j.bpc.2013.10.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/30/2013] [Accepted: 10/30/2013] [Indexed: 02/06/2023]
Abstract
Quadruplex priming amplification (QPA) allows isothermal amplification of nucleic acids with improved yield and simplified detection. This assay is based on a DNA quadruplex, GGGTGGGTGGGTGGG (G3T), which in the presence of specific cations possesses unusually high thermal stability. QPA employs truncated G3T sequences as primers, which upon polymerase elongation, self-dissociate from the binding site and allow the next round of priming without thermal unfolding of amplicons. The rate of amplification strongly depends on the thermal stability of the primer/primer binding site (PBS) complex and to date QPA has been demonstrated to work over a narrow temperature range. To expand the capabilities of QPA, in the present study, we studied the fold and thermodynamic properties of the wild-type G3T and variants containing sequence modifications or extensions at the 5'-end. Circular dichroism studies demonstrate that the substitution of thymidines by other nucleotides or GC addition at the 5'-end does not change the parallel fold of G3T. Thermal unfolding experiments revealed that purine bases incorporated at loop positions and 5'-end dinucleotide extension significantly destabilize the quadruplex, while loop pyrimidines have almost no effect. Overall, the results of these studies suggest that linear isothermal QPA can be performed over a wide temperature range to accommodate both thermophilic and mesophilic DNA polymerases.
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Affiliation(s)
- Jordan Mathias
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Robert Okyere
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Levan Lomidze
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - David Gvarjaladze
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Besik Kankia
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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