Viral Replication Complexes: Structures, Functions, Applications and Inhibitors David D. Boehr www.mdpi.com/journal/viruses Edited by Printed Edition of the Special Issue Published in Viruses viruses David D. Boehr (Ed.) Viral Replication Complexes: Structures, Functions, Applications and Inhibitors This book is a reprint of the Special Issue that appeared in the online, open access journal, Viruses (ISSN 1999-4915) in 2015 (available at: http://www.mdpi.com/journal/viruses/special_issues/replication-complexes). Guest Editor David D. Boehr The Pennsylvania State University USA Editorial Office MDPI AG Klybeckstrasse 64 Basel, Switzerland Publisher Shu-Kun Lin Managing Editor Delphine Guérin 1. Edition 2016 MDPI • Basel • Beijing • Wuhan • Barcelona ISBN 978-3-03842-167-2 (Hbk) ISBN 978-3-03842-168-9 (PDF) Articles in this volume are Open Access and distributed under the Creative Commons Attribution license (CC BY), which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. The book taken as a whole is © 2016 MDPI, Basel, Switzerland, distributed under the terms and conditions of the Creative Commons by Attribution (CC BY-NC-ND) license ( http://creativecommons.org/licenses/by -nc-nd/4.0/). III Table of Contents List of Contributors .................................................................................................... VII About the Guest Editor ............................................................................................. XIII Preface to “Viral Replication Complexes: Structures, Functions, Applications and Inhibitors“ ..................................................................................... XV Chapter 1: Molecular Perspectives on Virus Replication Proteins Cristina Ferrer-Orta, Diego Ferrero and Núria Verdaguer RNA-Dependent RNA Polymerases of Picornaviruses: From the Structure to Regulatory Mechanisms Reprinted from: Viruses 2015 , 7 (8), 4438–4460 http://www.mdpi.com/1999-4915/7/8/2829 .................................................................. 3 Ester Sesmero and Ian F. Thorpe Using the Hepatitis C Virus RNA-Dependent RNA Polymerase as a Model to Understand Viral Polymerase Structure, Function and Dynamics Reprinted from: Viruses 2015 , 7 (7), 3974–3994 http://www.mdpi.com/1999-4915/7/7/2808 ................................................................ 29 Xinran Liu, Derek M. Musser, Cheri A. Lee, Xiaorong Yang, Jamie J. Arnold, Craig E. Cameron and David D. Boehr Nucleobase but not Sugar Fidelity is Maintained in the Sabin I RNA-Dependent RNA Polymerase Reprinted from: Viruses 2015 , 7 (10), 5571–5586 http://www.mdpi.com/1999-4915/7/10/2894 .............................................................. 52 Ibrahim M. Moustafa, David W. Gohara, Akira Uchida, Neela Yennawar and Craig E. Cameron Conformational Ensemble of the Poliovirus 3CD Precursor Observed by MD Simulations and Confirmed by SAXS: A Strategy to Expand the Viral Proteome? Reprinted from: Viruses 2015 , 7 (11), 5962–5986 http://www.mdpi.com/1999-4915/7/11/2919 .............................................................. 74 IV Chapter 2: Coordinated Interactions of Viral Proteins and Nucleic Acids Erin Noble, Michelle M. Spiering and Stephen J. Benkovic Coordinated DNA Replication by the Bacteriophage T4 Replisome Reprinted from: Viruses 2015 , 7 (6), 3186–3200 http://www.mdpi.com/1999-4915/7/6/2766 ...............................................................111 Jason W. Rausch and Stuart F. J. Le Grice HIV Rev Assembly on the Rev Response Element (RRE): A Structural Perspective Reprinted from: Viruses 2015 , 7 (6), 3053–3075 http://www.mdpi.com/1999-4915/7/6/2760 ...............................................................127 Bárbara Rojas-Araya, Théophile Ohlmann and Ricardo Soto-Rifo Translational Control of the HIV Unspliced Genomic RNA Reprinted from: Viruses 2015 , 7 (8), 4326–4351 http://www.mdpi.com/1999-4915/7/8/2822 ...............................................................153 Valerie J. Klema, Radhakrishnan Padmanabhan and Kyung H. Choi Flaviviral Replication Complex: Coordination between RNA Synthesis and 5’- RNA Capping Reprinted from: Viruses 2015 , 7 (8), 4640–4656 http://www.mdpi.com/1999-4915/7/8/2837 ...............................................................180 Alexandre Carpentier, Pierre-Yves Barez, Malik Hamaidia, Hélène Gazon, Alix de Brogniez, Srikanth Perike, Nicolas Gillet and Luc Willems Modes of Human T Cell Leukemia Virus Type 1 Transmission, Replication and Persistence Reprinted from: Viruses 2015 , 7 (7), 3603–3624 http://www.mdpi.com/1999-4915/7/7/2793 ...............................................................198 V Chapter 3: Interplay Between Virus and Host in Virus Replication Santiago Guerrero, Julien Batisse, Camille Libre, Serena Bernacchi, Roland Marquet and Jean-Christophe Paillart HIV-1 Replication and the Cellular Eukaryotic Translation Apparatus Reprinted from: Viruses 2015 , 7 (1), 199–218 http://www.mdpi.com/1999-4915/7/1/199 .................................................................223 Luc Willems and Nicolas Albert Gillet APOBEC3 Interference during Replication of Viral Genomes Reprinted from: Viruses 2015 , 7 (6), 2999–3018 http://www.mdpi.com/1999-4915/7/6/2757 ...............................................................244 Jun Xiao, Jiang Deng, Liping Lv, Qiong Kang, Ping Ma, Fan Yan, Xin Song, Bo Gao, Yanyu Zhang and Jinbo Xu Hydrogen Peroxide Induce Human Cytomegalovirus Replication through the Activation of p38-MAPK Signaling Pathway Reprinted from: Viruses 2015 , 7 (6), 2816–2833 http://www.mdpi.com/1999-4915/7/6/2748 ...............................................................266 Meng Zhu, Hao Duan, Meng Gao, Hao Zhang and Yihong Peng Both ERK1 and ERK2 Are Required for Enterovirus 71 (EV71) Efficient Replication Reprinted from: Viruses 2015 , 7 (3), 1344–1356 http://www.mdpi.com/1999-4915/7/3/1344 ...............................................................285 Chapter 4: Virus Replication Organelles Colleen R. Reid, Adriana M. Airo and Tom C. Hobman The Virus-Host Interplay: Biogenesis of +RNA Replication Complexes Reprinted from: Viruses 2015 , 7 (8), 4385–4413 http://www.mdpi.com/1999-4915/7/8/2825 ...............................................................301 Evan D. Rossignol, Jie E. Yang and Esther Bullitt The Role of Electron Microscopy in Studying the Continuum of Changes in Membranous Structures during Poliovirus Infection Reprinted from: Viruses 2015 , 7 (10), 5305–5318 http://www.mdpi.com/1999-4915/7/10/2874 .............................................................332 VI Yu-Fu Hung, Melanie Schwarten, Silke Hoffmann, Dieter Willbold, Ella H. Sklan and Bernd W. Koenig Amino Terminal Region of Dengue Virus NS4A Cytosolic Domain Binds to Highly Curved Liposomes Reprinted from: Viruses 2015 , 7 (7), 4119–4130 http://www.mdpi.com/1999-4915/7/7/2812 ...............................................................351 Chapter 5: Antiviral Drugs Lei Kang, Jiaqian Pan, Jiaofen Wu, Jiali Hu, Qian Sun and Jing Tang Anti-HBV Drugs: Progress, Unmet Needs, and New Hope Reprinted from: Viruses 2015 , 7 (9), 4960–4977 http://www.mdpi.com/1999-4915/7/9/2854 ...............................................................367 Lonneke van der Linden, Katja C. Wolthers and Frank J.M. van Kuppeveld Replication and Inhibitors of Enteroviruses and Parechoviruses Reprinted from: Viruses 2015 , 7 (8), 4529–4562 http://www.mdpi.com/1999-4915/7/8/2832 ...............................................................391 VII List of Contributors Adriana M. Airo Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada. Jamie J. Arnold Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. Pierre-Yves Barez Molecular and Cellular Epigenetics (GIGA) and Molecular Biology (Gembloux Agro-Bio Tech), University of Liège (ULg), 4000 Liège, Belgium. Julien Batisse Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France. Stephen J. Benkovic Pennsylvania State University, Department of Chemistry, 414 Wartik Laboratory, University Park, PA 16802, USA. Serena Bernacchi Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France. David D. Boehr Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA. Esther Bullitt Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, W302, Boston, MA 02118-2526, USA. Craig E. Cameron Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. Alexandre Carpentier Molecular and Cellular Epigenetics (GIGA) and Molecular Biology (Gembloux Agro-Bio Tech), University of Liège (ULg), 4000 Liège, Belgium. Kyung H. Choi Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX 77555-0647, USA. Alix de Brogniez Molecular and Cellular Epigenetics (GIGA) and Molecular Biology (Gembloux Agro-Bio Tech), University of Liège (ULg), 4000 Liège, Belgium. Jiang Deng Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing 100850, China; Beijing Institute of Transfusion Medicine, 27 (9) Taiping Road, Beijing 100850, China. Hao Duan Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China. VIII Diego Ferrero Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park (PCB), Baldiri i Reixac 10, Barcelona E-08028, Spain. Cristina Ferrer-Orta Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park (PCB), Baldiri i Reixac 10, Barcelona E-08028, Spain. Bo Gao Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing 100850, China; Beijing Institute of Transfusion Medicine, 27 (9) Taiping Road, Beijing 100850, China. Meng Gao Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China. Hélène Gazon Molecular and Cellular Epigenetics (GIGA) and Molecular Biology (Gembloux Agro-Bio Tech), University of Liège (ULg), 4000 Liège, Belgium. Nicolas Gillet Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Liège (ULg), 13 avenue Maréchal Juin, Gembloux 5030, Belgium; Molecular and Cellular Epigenetics (GIGA) and Molecular Biology (Gembloux Agro-Bio Tech), University of Liège (ULg), 4000 Li è ge, Belgium. David W. Gohara Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, 1100 South Grand Ave, St Louis, MO 63104, USA. Stuart F. J. Le Grice Reverse Transcriptase Biochemistry Section, Basic Research Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA. Santiago Guerrero Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France; Present Address: Centre for Genomic Regulation, Dr. Aiguader, 88, PRBB Building, 08003 Barcelona, Spain. Malik Hamaidia Molecular and Cellular Epigenetics (GIGA) and Molecular Biology (Gembloux Agro-Bio Tech), University of Liège (ULg), 4000 Liège, Belgium. Tom C. Hobman Department of Cell Biology; Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada. Silke Hoffmann Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany. Jiali Hu Department of Pharmacy, The Third Staff Hospital of Baogang Group, 15 Qingnian Road, Baotou 014010, China. IX Yu-Fu Hung Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich,52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1,40255 Düsseldorf, Germany. Lei Kang Department of Clinical Pharmacy, Shanghai First People's Hospital, Shanghai Jiao Tong University, 650 New Songjiang Road, Songjiang District, Shanghai 201620, China. Qiong Kang Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing 100850, China; Beijing Institute of Transfusion Medicine, 27 (9) Taiping Road, Beijing 100850, China. Valerie J. Klema Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX 77555-0647, USA. Bernd W. Koenig Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich,52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1,40255 Düsseldorf, Germany. Cheri A. Lee Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. Camille Libre Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France. Lonneke van der Linden Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, Amsterdam 1105 AZ, The Netherlands. Xinran Liu Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA. Liping Lv Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing 100850, China; Beijing Institute of Transfusion Medicine, 27 (9) Taiping Road, Beijing 100850, China. Ping Ma Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing 100850, China; Beijing Institute of Transfusion Medicine, 27 (9) Taiping Road, Beijing 100850, China. Roland Marquet Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France. X Ibrahim M. Moustafa Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. Derek M. Musser Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA. Erin Noble Pennsylvania State University, Department of Chemistry, 414 Wartik Laboratory, University Park, PA 16802, USA. Théophile Ohlmann CIRI, International Center for Infectiology Research, Université de Lyon, Lyon 69007, France; Inserm, U1111, Lyon 69007, France; Ecole Normale Supérieure de Lyon, Lyon 69007, France; Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69007, France; CNRS, UMR5308, Lyon 69007, France. Radhakrishnan Padmanabhan Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, DC 20057, USA. Jean-Christophe Paillart Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France. Jiaqian Pan Department of Clinical Pharmacy, Shanghai First People's Hospital, Shanghai Jiao Tong University, 650 New Songjiang Road, Songjiang District, Shanghai 201620, China. Yihong Peng Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China. Srikanth Perike Molecular and Cellular Epigenetics (GIGA) and Molecular Biology (Gembloux Agro-Bio Tech), University of Liège (ULg), 4000 Liège, Belgium. Jason W. Rausch Reverse Transcriptase Biochemistry Section, Basic Research Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA. Colleen R. Reid Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada. Bárbara Rojas-Araya Molecular and Cellular Virology Laboratory, Program of Virology, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Independencia 834100, Santiago, Chile. Evan D. Rossignol Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, W302, Boston, MA 02118-2526, USA. Melanie Schwarten Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany. XI Ester Sesmero Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA. Ella H. Sklan Department Clinical Microbiology and Immunology, Sackler School of Medicine,Tel Aviv University, Tel Aviv 69978, Israel. Xin Song Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing 100850, China; Beijing Institute of Transfusion Medicine, 27 (9) Taiping Road, Beijing 100850, China. Ricardo Soto-Rifo Molecular and Cellular Virology Laboratory, Program of Virology, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Independencia 834100, Santiago, Chile. Michelle M. Spiering Pennsylvania State University, Department of Chemistry, 414 Wartik Laboratory, University Park, PA 16802, USA. Qian Sun Department of Clinical Pharmacy, Shanghai First People's Hospital, Shanghai Jiao Tong University, 650 New Songjiang Road, Songjiang District, Shanghai 201620, China. Jing Tang Department of Clinical Pharmacy, Shanghai First People's Hospital, Shanghai Jiao Tong University, 650 New Songjiang Road, Songjiang District, Shanghai 201620, China. Ian F. Thorpe Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA. Akira Uchida Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. Frank J.M. van Kuppeveld Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, Utrecht 3584 CL, The Netherlands. Núria Verdaguer Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park (PCB), Baldiri i Reixac 10, Barcelona E-08028, Spain. Dieter Willbold Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1,40255 Düsseldorf, Germany. Luc Willems Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Liège (ULg), 13 avenue Maréchal Juin, Gembloux 5030, Belgium; Molecular and Cellular Epigenetics (GIGA) and Molecular Biology (Gembloux Agro-Bio Tech), University of Liège (ULg), 4000 Li è ge, Belgium. XII Katja C. Wolthers Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, Amsterdam 1105 AZ, The Netherlands. Jiaofen Wu Department of Pharmacy, Ningbo Medical Treatment Center Lihuili Hospital, 57 Xingning Road, Ningbo 315040, China. Jun Xiao Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing 100850, China; Beijing Institute of Transfusion Medicine, 27 (9) Taiping Road, Beijing 100850, China. Jinbo Xu Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing 100850, China; Beijing Institute of Transfusion Medicine, 27 (9) Taiping Road, Beijing 100850, China. Fan Yan Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing 100850, China; Beijing Institute of Transfusion Medicine, 27 (9) Taiping Road, Beijing 100850, China. Jie E. Yang Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, W302, Boston, MA 02118-2526, USA. Xiaorong Yang Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA. Neela Yennawar Huck Institutes of life sciences, The Pennsylvania State University, University Park, PA 16802, USA. Hao Zhang Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China. Yanyu Zhang Beijing Key Laboratory of Blood Safety and Supply Technologies, Beijing 100850, China; Beijing Institute of Transfusion Medicine, 27 (9) Taiping Road, Beijing 100850, China. Meng Zhu Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China. XIII About the Guest Editor David D. Boehr , PhD, is currently an Associate Professor in the Department of Chemistry at the Pennsylvania State University. His PhD research focused on the study of antibiotic resistance enzymes, under the guidance of Dr. Gerard Wright at McMaster University in Canada. He also conducted postdoctoral research on the biophysical characterization of enzymes using solution-state Nuclear Magnetic Resonance with Dr. Peter Wright at The Scripps Research Institute. David's current research has focused on understanding protein structure, dynamics, regulation and binding interactions of viral proteins, particularly the RNA-dependent RNA polymerase. Other research interests include understanding amino acid interaction networks and the control of structural dynamics of enzymes towards enzyme engineering applications. XV Preface to “Viral Replication Complexes: Structures, Functions, Applications and Inhibitors” Viruses are obligate intracellular parasites that need to co-opt a living cell's machinery for replication. At the heart of the viral replication machinery are the nucleic acid polymerases, which are responsible for efficiently copying the viral genome. This process must often be coordinated with other viral processes, including protein translation and viral packaging. The polymerases and other components of the replication machinery may serve as potential anti-viral targets. Chapter 1 of this book is devoted to the basic structure -function relationships of viral nucleic acid polymerases and related proteins. Chapter 2 then discusses how interactions between the viral polymerase and viral nucleic acids and other proteins help to coordinate nucleic acid synthesis and other important viral processes. Chapter 3 builds on this discussion by including the roles of host proteins in these processes. Many viruses also co-opt host lipid membranes to provide more conducive environments for RNA synthesis and virus replication, which is discussed in Chapter 4. Finally, many of the processes discussed in the preceding chapters are potential antiviral drug targets, which is discussed in Chapter 5. David D. Boehr Guest Editor Chapter 1: Molecular Perspectives on Virus Replication Proteins RNA-Dependent RNA Polymerases of Picornaviruses: From the Structure to Regulatory Mechanisms Cristina Ferrer-Orta, Diego Ferrero and Núria Verdaguer Abstract: RNA viruses typically encode their own RNA-dependent RNA polymerase (RdRP) to ensure genome replication within the infected cells. RdRP function is critical not only for the virus life cycle but also for its adaptive potential. The combination of low fidelity of replication and the absence of proofreading and excision activities within the RdRPs result in high mutation frequencies that allow these viruses a rapid adaptation to changing environments. In this review, we summarize the current knowledge about structural and functional aspects on RdRP catalytic complexes, focused mainly in the Picornaviridae family. The structural data currently available from these viruses provided high-resolution snapshots for a range of conformational states associated to RNA template-primer binding, rNTP recognition, catalysis and chain translocation. As these enzymes are major targets for the development of antiviral compounds, such structural information is essential for the design of new therapies. Reprinted from Viruses Cite as: Ferrer-Orta, C.; Ferrero, D.; Verdaguer, N. RNA-Dependent RNA Polymerases of Picornaviruses: From the Structure to Regulatory Mechanisms. Viruses 2015 , 7 , 4438–4460. 1. Introduction RNA dependent RNA polymerases (RdRPs) are the catalytic components of the RNA replication and transcription machineries and the central players in the life cycle of RNA viruses. RdRPs belong to the superfamily of template-directed nucleic acid polymerases, including DNA-dependent DNA polymerases (DdDP), DNA-dependent RNA polymerases and Reverse Transcriptases (RT). All these enzymes share a cupped right hand structure, including fingers, palms and thumb domains, and catalyze phosphodiester bond formation through a conserved two-metal ion mechanism [ 1 ]. A structural feature unique to RdRPs is the “closed-hand” conformation, in opposition to the “open-hand” found in other polynucleotide polymerases. This “close-hand” conformation is accomplished by interconnecting the finger and thumb domains through the N-terminal portion of the protein and several loops protruding from fingers, named the fingertips that completely encircle the active site of the enzyme [ 2 , 3 ]. In the prototypic RdRPs the closed “right hand” architecture encircles seven motifs (A to G) conserved in sequence 3