DOCSLIB.ORG

HIV-1 Viral Infectivity Factor Recruitment of Cellular Protein

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
HIV-1 Viral Infectivity Factor Recruitment of Cellular Protein HIV-1 Viral Infectivity Factor Recruitment of Cellular Protein Complexes to Counter Host Antiviral Response By Sean L. Evans A dissertation submitted to Johns Hopkins University in conformity with requirements for the degree of Doctor of Philosophy Baltimore, Maryland February 2014 ©2014 Sean L. Evans All Rights Reserved ABSTRACT Human cytidine deaminase apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like 3 (APOBEC3) proteins (e.g. APOBEC3G) provide a potent host defense against HIV, in the absence of viral infectivity factor (Vif). These antiviral proteins induce nucleotide modifications, specifically converting cytosines to uracils in newly synthesized minus-strand viral DNA during the HIV reverse transcription process, ultimately resulting in abortive viral infection. HIV must overcome this and other host defenses to successfully replicate and spread. HIV- 1 encodes the Vif protein, which binds and suppresses the antiviral effects of select APOBEC3 proteins by targeting them for degradation through the 26S proteasome enabling the virus to carry out a productive infection. Our lab was the first to demonstrate that Vif recruits cellular Cullin5 (Cul5), Elongin B (Elo B), and Elongin C (Elo C) to form a viral E3 ubiquitin ligase to target APOBEC3 proteins for polyubiquitination and degradation. Recently, we reported the direct interaction between Vif and a previously unknown binding partner and regulator of Vif-induced APOBEC3 degradation, core binding factor beta (CBF-β). This dissertation reports on the functional importance of the Vif:CBF-β interaction and characterizes this interaction using fluorescence imaging and functional assays in mammalian cells as well as in vitro over-expressed protein complex binding studies (Chapter 3). Next, the E3 ligase components that bind Vif have ii long been thought to require residues in Vif’s C-terminus, exclusively. However, this report provides evidence that the Vif:Cul5 interaction also requires a motif in Vif’s N-terminus (Chapter 4). Recognizing the importance for these multiple points of interaction between Vif and the E3 ligase, a rapid in vitro fluorescence based inhibitor assay was developed to identify small-molecule inhibitors of the Vif:CBF-β and Vif:Cul5 interaction with the ultimate goal of developing novel anti- HIV therapeutic compounds (Chapter 5). Finally, this report discusses a novel role for Vif as a transcriptional enhancer when in complex with the heterodimeric transcription factor RUNX:CBF-β. The Vif:RUNX:CBF-β complex appears to up- regulate cytokines that may facilitate HIV replication (Chapter 6). The critical role that Vif plays during HIV infection demonstrates its potential utility as a novel HIV therapeutic target. Advisor: Xiao-Fang Yu iii ACKNOWLEDGEMENTS I must first start by acknowledging both my father and mother. To my late mother, I wish you could have been here to witness this moment in my life. You taught me how to be an independent, responsible and hard-working person, skills that have been essential for surviving graduate school and life. To my father, thank you for encouraging me to follow my dreams and interests. To both of you, thank you for providing me with a rich environment of love and resources to thrive in my pursuits. I owe you both a lifetime of gratitude for providing me the resources and support to allow me to reach this achievement in my life. To my advisor, Dr. Xiao-Fang Yu, I thank you for encouraging and fostering my scientific curiosity. I am grateful for the degree of intellectual freedom that you have afforded me. Your support has given me the ability to grow as a scientist, which I am forever grateful. In addition, I would like to thank my dissertation committee members: Drs. Egbert Hoiczyk, Alan Friedman, and Michael Matunis for your invaluable suggestions, advice and encouraging words throughout my time in graduate school. In addition, I would like to thank Drs. Amanda Brown, Andrew Pekosz and Fengyi Wan for agreeing to serve as alternate committee members. I would also like to thank the administrators who have helped me through grant applications as well as general graduate school and lab administrative items: special thanks to Patricia Bazemore, Joan Evans, and Gail O’Connor. iv To the members of the Yu lab both past and present, thank you for contributing to an environment where science and collaboration are not only possible but also enjoyable. To my colleague, mentor, and friend, Anjie Zhen, you provided the initial technical support, which provided an excellent foundation in how to successfully plan and execute experiments. Without this and your continued support after graduating, I may have never been able to successfully finish graduate school. Additionally, there have been so many wonderful collaborators that have contributed to the work presented in this thesis: Arne Schön, Jason Huska, Qimeng Gao, Yayan Liu, and Wenyan Zhang. In addition, my time would not have been the same without Xiaohong Zhou, Xue Han, Ke Zhao, Du Juan, Wei Wei, Qimeng Gao and Haoran Guo. You have all made me feel very welcome in our little “Chinatown” lab. Finally, I would like to thank additional family members and friends who have been another source of motivation and support throughout my life and time in graduate school. To my older sister, Alecia, we have been through so much together throughout our lives, and I am so thankful that you were there next to me. To Grandma Christine, Aunts & Uncles (Linda, Velma, Audrey, Pat, Ran, and Charlie Jr.), Destiny, cousins (Dom, Demetrius, Stacie, Kevin, Jarrod, and Dorothy), nephews/nieces (Zora, Zach Jr., and Alissa Grace), Zach Sr., Vicki, Jasmin, Jie, Amy, and Melissa, you all have been my greatest allies during graduate school. Thank you all so much for your love and support! v TABLE OF CONTENTS ABSTRACT .................................................................................................................................. ii ACKNOWLEDGEMENTS ......................................................................................................... iv TABLE OF CONTENTS ............................................................................................................. vi LIST OF TABLES .................................................................................................................... xiii LIST OF FIGURES .................................................................................................................. xiv COMMON ABBREVIATIONS ............................................................................................... xvi CHAPTER 1 ................................................................................................................................. 1 INTRODUCTION TO RETROVIRAL RESTRICTION FACTORS AND HIV COUNTER MEASURES CHAPTER 2 .............................................................................................................................. 50 GENERAL MATERIALS AND METHODS CHAPTER 3 .............................................................................................................................. 62 IDENTIFICATION OF NOVEL VIF BINDING PARTNER AND REGULATOR, CORE BINDING FACTOR BETA AND IN VITRO CHARACTERIZATION OF VIF:CBF-β:E3 LIGASE COMPLEXES CHAPTER 4 ............................................................................................................................ 101 VIF N-TERMINAL MOTIF IS REQUIRED FOR CUL5 BINDING CHAPTER 5 ............................................................................................................................ 138 vi DESIGN AND OPTIMIZATION OF IN VITRO PRIMARY HIGH-THROUGHPUT SCREEN FOR SMALL MOLECULE INHIBITORS OF VIF:CBF-β AND/OR VIF CUL5 INTERACTIONS CHAPTER 6 ............................................................................................................................ 148 NOVEL FUNCTIONS OF VIF IN COMPLEX WITH CBF-β:RUNX CHAPTER 7 ............................................................................................................................ 188 FUTURE DIRECTIONS REFERENCES ......................................................................................................................... 194 CURRICULUM VITAE ........................................................................................................... 225 vii CHAPTER 1 INTRODUCTION TO RETROVIRAL RESTRICTION FACTORS AND HIV COUNTER MEASURES 1.1 General Introduction 1.2 HIV Classification and Biology 1.3 HIV Transmission and Replication 1.4 Host Immune Response to HIV Infection 1.4.1 Host Intrinsic Restriction to Retroviruses and Viral Antagonism 1.5 Cellular E3 Ubiquitin Ligase 1.6 APOBEC3 and Vif 1.7 Project Goals and Aims CHAPTER 2 GENERAL MATERIALS AND METHODS 2.1 E. coli Plasmid Constructs, Expression, Purification, and Protein Visualization 2.2 Mammalian Cell Plasmid Constructs, Transfection, Expression, Immunoprecipitation and Protein Analysis 2.3 Antibodies CHAPTER 3 viii IN VITRO AND IN VIVO CHARACTERIZATION OF VIF:CBF-β:E3 LIGASE COMPLEXES Paper 1 – Zhang W., Du J., Evans SL., Yu Y., Yu X-F. T-cell differentiation factor CBF-β regulates HIV-1 Vif-mediated evasion of host restriction. Nature. Dec 2011. Paper 2 – Zhou X.*, Evans SL.*, Han X., Liu Y., Yu X-F. Characterization of the Interaction of Full Length HIV-1 Vif Protein with its Key Regulator CBF-β and CRL5 E3 Ubiquitin Ligase Components. PLoSOne. Mar 2012. 3.1 Introduction 3.1.1 Biochemical discovery of new Vif binding partner 3.1.2 Functional role in assisting Vif-induced
Load more

Recommended publications
  • Impact of Natural HIV-1 Nef Alleles and Polymorphisms on SERINC3/5 Downregulation
    Impact of natural HIV-1 Nef alleles and polymorphisms on SERINC3/5 downregulation by Steven W. Jin B.Sc., Simon Fraser University, 2016 Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science in the Master of Science Program Faculty of Health Sciences © Steven W. Jin 2019 SIMON FRASER UNIVERSITY Spring 2019 Copyright in this work rests with the author. Please ensure that any reproduction or re-use is done in accordance with the relevant national copyright legislation. Approval Name: Steven W. Jin Degree: Master of Science Title: Impact of natural HIV-1 Nef alleles and polymorphisms on SERINC3/5 downregulation Examining Committee: Chair: Kanna Hayashi Assistant Professor Mark Brockman Senior Supervisor Associate Professor Masahiro Niikura Supervisor Associate Professor Ralph Pantophlet Supervisor Associate Professor Lisa Craig Examiner Professor Department of Molecular Biology and Biochemistry Date Defended/Approved: April 25, 2019 ii Ethics Statement iii Abstract HIV-1 Nef is a multifunctional accessory protein required for efficient viral pathogenesis. It was recently identified that the serine incorporators (SERINC) 3 and 5 are host restriction factors that decrease the infectivity of HIV-1 when incorporated into newly formed virions. However, Nef counteracts these effects by downregulating SERINC from the cell surface. Currently, there lacks a comprehensive study investigating the impact of primary Nef alleles on SERINC downregulation, as most studies to date utilize lab- adapted or reference HIV strains. In this thesis, I characterized and compared SERINC downregulation from >400 Nef alleles isolated from patients with distinct clinical outcomes and subtypes. I found that primary Nef alleles displayed a dynamic range of SERINC downregulation abilities, thus allowing naturally-occurring polymorphisms that modulate this activity to be identified.
    [Show full text]
  • MS Ritgerð Aðalbjörg Aðalbjörnsdóttir
    The Vif protein of maedi-visna virus Protein interaction and new roles Aðalbjörg Aðalbjörnsdóttir Thesis for the degree of Master of Science University of Iceland Faculty of medicine School of Health Sciences Vif prótein mæði-visnuveiru Prótein tengsl og ný hlutverk Aðalbjörg Aðalbjörnsdóttir Ritgerð til meistaragráðu í Líf og læknavísindum Umsjónarkennari: Valgerður Andrésdóttir Meistaranámsnefnd: Stefán Ragnar Jónsson og Ólafur S. Andrésson Læknadeild Heilbrigðisvísindasvið Háskóla Íslands Júní 2016 The Vif protein of maedi-visna virus Protein interaction and new roles Aðalbjörg Aðalbjörnsdóttir Thesis for the degree of Master of Science Supervisor: Valgerður Andrésdóttir Masters committee: Stefán Ragnar Jónsson and Ólafur S. Andrésson Faculty of Medicine School of Health Sciences June 2016 Ritgerð þessi er til meistaragráðu í Líf og læknavísindum og er óheimilt að afrita ritgerðina á nokkurn hátt nema með leyfi rétthafa. © Aðalbjörg Aðalbjörnsdóttir 2016 Prentun: Háskólaprent Reykjavík, Ísland 2016 Ágrip Mæði-visnuveira (MVV) er lentiveira af ættkvísl retróveira. Hún veldur hæggengri lungnabólgu (mæði) og heilabólgu (visnu) í kindum. Aðalmarkfrumur veirunnar eru mónocytar/makrófagar. Veiran er náskyld HIV og hefur verið notuð sem módel fyrir HIV sýkingar. Stöðug vopnakapphlaup milli veira og fruma hafa leitt af sér fjölda sértækra aðferða í vörnum hýsilsfrumu gegn veirusýkingum. Fruman hefur þróað með sér innrænar varnir gegn ýmsum sýkingum. Þessar varnir geta verið mjög sérhæfðar og tjáning þeirra spilar stórt hlutverk í hvaða frumur er hægt að sýkja og hverjar ekki. Dæmi um slíkan frumubundinn þátt eru APOBEC3 próteinin. APOBEC3 próteinin eru fjölskylda cytósín deaminasa sem geta hindrað retróveirur og retróstökkla. Þetta gera þau með því að afaminera cýtósín í úrasil í einþátta DNA á meðan á víxlritun stendur og valda þar með G-A stökkbreytingum í forveirunni.
    [Show full text]
  • 718 HIV Disorders of the Brain; Pathology and Pathogenesis Luis
    [Frontiers in Bioscience 11, 718-732, January 1, 2006] HIV disorders of the brain; pathology and pathogenesis Luis Del Valle and Sergio Piña-Oviedo Center for Neurovirology and Cancer Biology, Laboratory of Neuropathology and Molecular Pathology, Temple University, 1900 North 12th Street, Suite 240, Philadelphia, Pennsylvania 19122 USA TABLE OF CONTENTS 1. Abstract 2. AIDS-Encephalopathy 2.1. Definition 2.2. HIV-1 Structure 2.3. Histopathology 2.4. Clinical Manifestations 2.5. Physiopathology 3. Progressive Multifocal Leukoencephalopathy 3.1. Definition 3.2. JC Virus Biological Considerations 3.3. JC Virus Structure 3.4. Histopathology 3.5. Clinical Manifestations 3.6. Physiopathology 4. Cryptococcosis 5.1. Definition 5.2. Cryptococcus neoformans Structure 5.3. Histopathology 5.4. Clinical Manifestations 5.5. Physiopathology 5. Toxoplasmosis 5.1. Definition 5.2. Toxoplasma godii Structure 5.3. Histopathology 5.4. Clinical Manifestations 5.5. Physiopathology 6. Primary CNS Lymphomas 6.1. Definition 6.2. Histopathology 6.3. Clinical Manifestations 6.4. Physiopathology 7. Acknowledgments 8. References 1. ABSTRACT Infection with HIV-1 has spread exponentially in still present in approximately 70 to 90% of patients and recent years to reach alarming proportions. It is estimated can be the result of HIV itself or of opportunistic than more than 33 million adults and 1.3 million children infections. Here we briefly review the pathology and are infected worldwide. Approximately 16,000 new cases pathophysiology of AIDS-Encephalopathy, of some of are diagnosed every day and almost 3 million people die the significant opportunistic infections affecting the every year from AIDS, making it the fourth leading brain in the context of AIDS, including Progressive cause of death in the world.
    [Show full text]
  • Herpes Simplex Virus Type 1 Oril Is Not Required for Virus Infection In
    JOURNAL OF VIROLOGY, Nov. 1987, p. 3528-3535 Vol. 61, No. 11 0022-538X/87/113528-08$02.00/0 Copyright C 1987, American Society for Microbiology Herpes Simplex Virus Type 1 oriL Is Not Required for Virus Replication or for the Establishment and Reactivation of Latent Infection in Mice MARYELLEN POLVINO-BODNAR, PAULO K. ORBERG, AND PRISCILLA A. SCHAFFER* Laboratory of Tumor Virus Genetics, Dana-Farber Cancer Institute, and Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115 Received 11 May 1987/Accepted 31 July 1987 During the course of experiments designed to isolate deletion mutants of herpes simplex virus type 1 in the gene encoding the major DNA-binding protein, ICP8, a mutant, d61, that grew efficiently in ICP8-expressing Vero cells but not in normal Vero cells was isolated (P. K. Orberg and P. A. Schaffer, J. Virol. 61:1136-1146, 1987). d61 was derived by cotransfection of ICP8-expressing Vero cells with infectious wild-type viral DNA and a plasmid, pDX, that contains an engineered 780-base-pair (bp) deletion in the ICP8 gene, as well as a spontaneous -55-bp deletion in OriL. Gel electrophoresis and Southern blot analysis indicated that d61 DNA carried both deletions present in pDX. The ability of d61 to replicate despite the deletion in OriL suggested that a functional OriL is not essential for virus replication in vitro. Because d61 harbored two mutations, a second mutant, ts+7, with a deletion in oriL-associated sequences and an intact ICP8 gene was constructed. Both d61 and ts+7 replicated efficiently in their respective permissive host cells, although their yields were slightly lower than those of control viruses with intact oriL sequences.
    [Show full text]
  • Foamy Virus Assembly with Emphasis on Pol Encapsidation
    Viruses 2013, 5, 886-900; doi:10.3390/v5030886 OPEN ACCESS viruses ISSN 1999-4915 www.mdpi.com/journal/viruses Review Foamy Virus Assembly with Emphasis on Pol Encapsidation Eun-Gyung Lee 1, Carolyn R. Stenbak 2 and Maxine L. Linial 1,* 1 Fred Hutchinson Cancer Research Center, Basic Sciences Division; 1100 Fairview Avenue North, Seattle, WA 98109, USA; E-Mails: [email protected] (EGL); [email protected] (MLL) 2 Seattle University, Biology Department; 901 12th Avenue, Seattle, WA 98122, USA; E-Mail: [email protected] * Authors to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-206- 667-4442; Fax: +1-206-667-5939 Received: 31 January 2013; in revised form: 11 March 2013 / Accepted: 14 March 2013 / Published: 20 March 2013 Abstract: Foamy viruses (FVs) differ from all other genera of retroviruses (orthoretroviruses) in many aspects of viral replication. In this review, we discuss FV assembly, with special emphasis on Pol incorporation. FV assembly takes place intracellularly, near the pericentriolar region, at a site similar to that used by betaretroviruses. The regions of Gag, Pol and genomic RNA required for viral assembly are described. In contrast to orthoretroviral Pol, which is synthesized as a Gag-Pol fusion protein and packaged through Gag-Gag interactions, FV Pol is synthesized from a spliced mRNA lacking all Gag sequences. Thus, encapsidation of FV Pol requires a different mechanism. We detail how WT Pol lacking Gag sequences is incorporated into virus particles. In addition, a mutant in which Pol is expressed as an orthoretroviral-like Gag-Pol fusion protein is discussed.
    [Show full text]
  • Topological Analysis of the Gp41 MPER on Lipid Bilayers Relevant to the Metastable HIV-1 Envelope Prefusion State
    Topological analysis of the gp41 MPER on lipid bilayers relevant to the metastable HIV-1 envelope prefusion state Yi Wanga,b, Pavanjeet Kaurc,d, Zhen-Yu J. Sune,1, Mostafa A. Elbahnasawya,b,2, Zahra Hayatic,d, Zhi-Song Qiaoa,b,3, Nhat N. Buic, Camila Chilea,b,4, Mahmoud L. Nasre,5, Gerhard Wagnere, Jia-Huai Wanga,f, Likai Songc, Ellis L. Reinherza,b,6, and Mikyung Kima,g,6 aLaboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115; bDepartment of Medicine, Harvard Medical School, Boston, MA 02115; cNational High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32306; dDepartment of Physics, Florida State University, Tallahassee, FL 32306; eDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; fDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215; and gDepartment of Dermatology, Harvard Medical School, Boston, MA 02215 Edited by Peter Palese, Icahn School of Medicine at Mount Sinai, New York, NY, and approved September 23, 2019 (received for review July 18, 2019) The membrane proximal external region (MPER) of HIV-1 envelope immunologically vulnerable epitopes targeted by several of the most glycoprotein (gp) 41 is an attractive vaccine target for elicitation of broadly neutralizing antibodies (bNAbs) developed during the broadly neutralizing antibodies (bNAbs) by vaccination. However, course of natural HIV-1 infection (10–13). Insertion, deletion, current details regarding the quaternary structural organization of and mutations of residues in the MPER defined the functional the MPER within the native prefusion trimer [(gp120/41)3] are elu- importance of the MPER in Env incorporation, viral fusion, and sive and even contradictory, hindering rational MPER immunogen infectivity (14–16).
    [Show full text]
  • UC Merced UC Merced Undergraduate Research Journal
    UC Merced UC Merced Undergraduate Research Journal Title Antiviral Drugs Targeting Host Proteins an Efficient Strategy Permalink https://escholarship.org/uc/item/66f5b4m0 Journal UC Merced Undergraduate Research Journal, 9(2) Author Karmonphet, Arrada Publication Date 2017 DOI 10.5070/M492034789 Undergraduate eScholarship.org Powered by the California Digital Library University of California Antiviral Drugs Targeting Host Proteins an Efficient Strategy Arrada Karmonphet University of California, Merced Keywords: Proteins, Viruses, Drugs 1 Abstract Viruses have the ability to spread rapidly because the proteins and enzymes from the host cell help in the development of viruses. Although there are many vaccines that can prevent some viruses from infecting the body, the antiviral drugs today have not been effective in combating viruses from the start of spreading. This is due to the fact that the processes inside a virus are still being studied. However, host proteins proved to be valuable factors responsible for viral replication and spreading. It was found that certain functions such as capsid formation of the virus utilized a biochemical pathway that involved host proteins and some proteins of the host cell were evolutionarily conserved. When the important host proteins were altered, or removed the viruses weren’t able to replicate as effectively. It was concluded that targeting the host proteins had a significant effect in viral replication. This approach can stop viral replication from the start, create less viral resistance, and help find new antiviral drugs that work for many different types of viruses. This review will analyze five research articles about protein interactions in viruses and how monitoring the proteins and biochemical pathways can lead to the discovery of druggable targets during development.
    [Show full text]
  • (Infected Cell Protein 8) of Herpes Simplex Virus L*
    THEJOURNAL OF BIOLOGICAL CHEMISTRY Vol. 262, No. 9, Issue of March 25, pp. 4260-4266, 1987 0 1987 by The American Society of Biological Chemists, Inc Printed in U.S. A. Interaction between theDNA Polymerase and Single-stranded DNA- binding Protein (Infected Cell Protein 8) of Herpes Simplex Virus l* (Received for publication, September 22, 1986) Michael E. O’DonnellS, Per EliasQ,Barbara E. Funnellll, and I. R. Lehman From the Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305 The herpes virus-encoded DNA replication protein, ICP8 completely inhibits replication of singly primed ssDNA infected cell protein 8 (ICPS), binds specifically to templates by the herpespolymerase. On the other hand, ICP8 single-stranded DNA with a stoichiometry of one ICPS strongly stimulates replication of duplex DNA. It does so, molecule/l2 nucleotides. In the absence of single- however, onlyin the presence of anuclear extract from stranded DNA, it assembles into long filamentous herpes-infected cells. structures. Binding of ICPS inhibits DNA synthesis by the herpes-induced DNA polymerase on singly primed EXPERIMENTALPROCEDURES single-stranded DNA circles. In contrast, ICPS greatly Materials-DNase I and venom phosphodiesterase were obtained stimulates replication of circular duplex DNA by the from Worthington. The syntheticoligodeoxynucleotide (44-mer) was polymerase. Stimulation occurs only in the presence of synthesized by the solid-phase coupling of protected phosphoramidate a nuclear extract from herpes-infected cells. Appear- nucleoside derivatives (11).3H-Labeled #X ssDNA was a gift from ance of the stimulatory activity in nuclear extracts Dr. R. Bryant (this department). pMOB45 (10.5 kilobases) linear coincides closely with the time of appearance of her- duplex plasmid DNA was a gift from Dr.
    [Show full text]
  • Assessment of the Interaction Between the Human
    VARIATIONS IN THE V3 CROWN OF HIV-1 ENVELOPE IMPACT AFFINITY FOR CCR5 AND AFFECT ENTRY AND REPLICATIVE FITNESS By MICHAEL ANDREW LOBRITZ Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Dissertation advisor: Eric J. Arts, Ph.D. Department of Molecular Biology and Microbiology CASE WESTERN RESERVE UNIVERSITY August 2007 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the dissertation of ______________________________________________________ candidate for the Ph.D. degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. Table of Contents Chapter 1: Introduction........................................................................................................................16 1.A. HIV and AIDS..............................................................................................17 1.B. Retroviruses: Structure, Organization, and Replication...............................20 1.B.1. HIV-1 Genome...............................................................................20 1.B.2. HIV-1 Particle................................................................................23
    [Show full text]
  • Autophagy and Mammalian Viruses: Roles in Immune Response, Viral Replication, and Beyond
    Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2016 Autophagy and mammalian viruses: roles in immune response, viral replication, and beyond Paul, P ; Münz, C Abstract: Autophagy is an important cellular catabolic process conserved from yeast to man. Double- membrane vesicles deliver their cargo to the lysosome for degradation. Hence, autophagy is one of the key mechanisms mammalian cells deploy to rid themselves of intracellular pathogens including viruses. How- ever, autophagy serves many more functions during viral infection. First, it regulates the immune response through selective degradation of immune components, thus preventing possibly harmful overactivation and inflammation. Additionally, it delivers virus-derived antigens to antigen-loading compartments for presentation to T lymphocytes. Second, it might take an active part in the viral life cycle by, eg, facili- tating its release from cells. Lastly, in the constant arms race between host and virus, autophagy is often hijacked by viruses and manipulated to their own advantage. In this review, we will highlight key steps during viral infection in which autophagy plays a role. We have selected some exemplary viruses and will describe the molecular mechanisms behind their intricate relationship with the autophagic machinery, a result of host–pathogen coevolution. DOI: https://doi.org/10.1016/bs.aivir.2016.02.002 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-131236 Book Section Accepted Version The following work is licensed under a Creative Commons: Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) License.
    [Show full text]
  • Role of Reverse Transcriptase and APOBEC3G in Survival of Human
    & My gy co lo lo ro g i y V Soni et al., Virol Mycol 2013, 3:1 Virology & Mycology DOI: 10.4172/2161-0517.1000125 ISSN: 2161-0517 Review Article Open Access Role of Reverse Transcriptase and APOBEC3G in Survival of Human Immune Deficiency Virus -1 Genome Raj Kumar Soni*, Amol Kanampalliwar and Archana Tiwari School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya (State Technological University), Madhya Pradesh, India Abstract Development of an effective vaccine against HIV-1 is a major challenge for scientists at present. Rapid mutation and replication of the virus in patients contribute to the evolution of the virus, which makes it unconquerable. Hence a deep understanding of critical elements related to HIV-1 is necessary. Errors introduced during DNA synthesis by reverse transcriptase are the primary source of genetic variation within retroviral populations. Numerous current studies have shown that apolipo protein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3G) proteins mediated sub- lethal mutagenesis of HIV-1 proviral DNA contributes in viral fitness by accelerating human immunodeficiency virus-1 evolution. This results in the loss of the immunity and development of resistance against anti-viral drugs. This review focuses on the latest biological, biochemical, and structural studies in an attempt to discuss current ideas related to mutations initiated by reverse transcriptase and APOBEC3G. It also describes their effect on immunological diversity and retroviral restriction, and their overall effect on the viral genome respectively. A new procedure for eradication of HIV-1 has also been proposed based on the previous studies and proven facts. Keywords: HIV-1; Reverse transcriptase; Recombination; defined.
    [Show full text]
  • Enzyme Activities in Four Different Forms of Human Immunodeficiency
    Proc. Nati. Acad. Sci. USA Vol. 88, pp. 45%-4600, June 1991 Biochemistry Enzyme activities in four different forms of human immunodeficiency virus 1 poi gene products (reverse transcriptase/RNase H/crossover linker mutagenesis/baculoirus expression system) YU-WEN HU AND C. YONG KANG Department of Microbiology and Immunology, University of Ottawa, Faculty of Medicine, Ottawa, ON, Canada K1H 8M5 Communicated by Max D. Summers, February 19, 1991 (received for review December 3, 1990) ABSTRACT Five cassettes of the pol gene of human im- activity (10, 11) but no RNase H activity (3, 7, 12, 13). The munodeficiency virus 1 were constructed and inserted under reverse transcriptase isolated from purified HIV-1 has a the control of the polyhedrin gene promoter of Autographa molecular mass of 95 (14) to 110 (15) kDa, as determined by calfornica nuclear polyhedrosis virus by homologous recom- gel filtration and glycerol gradient centrifugation, respec- bination. The first cassette polF contains the full-length pol tively. However, the 98-kDa nonprocessed polyprotein ex- open reading frame; the second cassette pollOO starts with the pressed in Escherichia coli displayed little or no reverse first AUG codon of the pol gene and deletes 103 amino acids transcriptase activity (16). The p66/pSi heterodimer ex- from the amino terminus of the pol gene product; the third pressed in E. coli has an apparent molecular mass of 120-130 cassette po197 deletes the entire protease coding sequence; the kDa and was active (5, 6). In addition, there is a 165-kDa fourth cassette po166 deletes both the protease and endonucle- putative gag-pol precursor polyprotein that also possesses ase/integrase coding sequences; and the fifth cassette polSl reverse transcriptase activity (10).
    [Show full text]