Multiple Cellular Proteins Interact with LEDGF/P75 Through a Conserved Unstructured Consensus Motif
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Dissertation Philip Böhler
Three Tales of Death: New Pathways in the Induction, Inhibition and Execution of Apoptosis Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Heinrich-Heine-Universität Düsseldorf vorgelegt von Philip Böhler aus Bonn Düsseldorf, Juni 2019 aus dem Institut für Molekulare Medizin I der Heinrich-Heine-Universität Düsseldorf Gedruckt mit der Genehmigung der Mathematisch-Naturwissenschaftlichen Fakultät der Heinrich-Heine-Universität Düsseldorf Berichterstatter: 1. Prof. Dr. Sebastian Wesselborg 2. Prof. Dr. Henrike Heise Tag der mündlichen Prüfung: 29. Oktober 2019 “Where the first primal cell was, there was I also. Where man is, there am I. When the last life crawls under freezing stars, there will I be.” — DEATH, in: Mort, by Terry Pratchett “Right away I found out something about biology: it was very easy to find a question that was very interesting, and that nobody knew the answer to.” — Richard Feynman, in: Surely You're Joking, Mr. Feynman! Acknowledgements (Danksagung) Acknowledgements (Danksagung) Viele Menschen haben zum Gelingen meiner Forschungsarbeit und dieser Dissertation beigetragen, und nicht alle können hier namentlich erwähnt werden. Dennoch möchte ich einige besonders hervorheben. An erster Stelle möchte ich Professor Sebastian Wesselborg danken, der diese Dissertation als Erstgutachter betreut hat und der mir die Möglichkeit gab, die dazugehörigen experimentellen Arbeiten am Institut für Molekulare Medizin durchzuführen. Er und Professor Björn Stork, dem ich für die herzliche Aufnahme in seine Arbeitsgruppe danke, legten durch die richtige Mischung aus aktiver Förderung und dem Freiraum zur Umsetzung eigener wissenschaftlicher Ideen die ideale Grundlage für die Forschungsprojekte, aus denen diese Dissertation entstand. Professorin Henrike Heise, die sich freundlicherweise zur Betreuung dieser Dissertation als Zweitgutachterin bereiterklärt hat, gilt ebenfalls mein herzlicher Dank. -
Characterization of the Matrix Proteins of the Fish Rhabdovirus, Infectious Hematopoietic Necrosis Virus
AN ABSTRACT OF THE THESIS OF Patricia A. Ormonde for the degree of Master of Science presented on April 14. 1995. Title: Characterization of the Matrix Proteins of the Fish Rhabdovinis, Infectious Hematopoietic Necrosis Virus. Redacted for Privacy Abstract approved: Jo-Ann C. ong Infectious hematopoietic necrosis virus (1HNV) is an important fish pathogen enzootic in salmon and trout populations of the Pacific Northwestern United States. Occasional epizootics in fish hatcheries can result in devastating losses of fish stocks. The complete nucleotide sequence of IHNV has not yet been determined. This knowledge is the first step towards understanding the roles viral proteins play in IHNV infection, and is necessary for determining the relatedness of IHNV to other rhabdoviruses. The glycoprotein, nucleocapsid and non-virion genes of IHNV have been described previously; however, at the initiation of this study, very little was known about the matrix protein genes. Rhabdoviral matrix proteins have been found to be important in viral transcription and virion assembly. This thesis describes the preliminary characterization of the M1 and M2 matrix proteins of IHNV. In addition, the trout humoral immune response to M1 and M2 proteins expressed from plasmid DNA injected into the fish was investigated. This work may prove useful in designing future vaccines against IHN. The sequences of M1 phosphoprotein and M2 matrix protein genes of IHNV were determined from both genomic and mRNA clones. Analysis of the sequences indicated that the predicted open reading frame of M1 gene encoded a 230 amino acid protein with a estimated molecular weight of 25.6 kDa. Further analysis revealed a second open reading frame encoding a 42 amino acid protein with a calculated molecular weight of 4.8 kDa. -
Viral Strategies to Arrest Host Mrna Nuclear Export
Viruses 2013, 5, 1824-1849; doi:10.3390/v5071824 OPEN ACCESS viruses ISSN 1999-4915 www.mdpi.com/journal/viruses Review Nuclear Imprisonment: Viral Strategies to Arrest Host mRNA Nuclear Export Sharon K. Kuss *, Miguel A. Mata, Liang Zhang and Beatriz M. A. Fontoura Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; E-Mails: [email protected] (M.A.M.); [email protected] (L.Z.); [email protected] (B.M.A.F) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-214-633-2001; Fax: +1-214-648-5814. Received: 10 June 2013; in revised form: 27 June 2013 / Accepted: 11 July 2013 / Published: 18 July 2013 Abstract: Viruses possess many strategies to impair host cellular responses to infection. Nuclear export of host messenger RNAs (mRNA) that encode antiviral factors is critical for antiviral protein production and control of viral infections. Several viruses have evolved sophisticated strategies to inhibit nuclear export of host mRNAs, including targeting mRNA export factors and nucleoporins to compromise their roles in nucleo-cytoplasmic trafficking of cellular mRNA. Here, we present a review of research focused on suppression of host mRNA nuclear export by viruses, including influenza A virus and vesicular stomatitis virus, and the impact of this viral suppression on host antiviral responses. Keywords: virus; influenza virus; vesicular stomatitis virus; VSV; NS1; matrix protein; nuclear export; nucleo-cytoplasmic trafficking; mRNA export; NXF1; TAP; CRM1; Rae1 1. Introduction Nucleo-cytoplasmic trafficking of proteins and RNA is critical for proper cellular functions and survival. -
Synthesis and Processing of the Transmembrane Envelope Protein of Equine Infectious Anemia Virus NANCY R
JOURNAL OF VIROLOGY, Aug. 1990, p. 3770-3778 Vol. 64, No. 8 0022-538X/90/083770-09$02.00/0 Copyright C 1990, American Society for Microbiology Synthesis and Processing of the Transmembrane Envelope Protein of Equine Infectious Anemia Virus NANCY R. RICE,'* LOUIS E. HENDERSON,' RAYMOND C. SOWDER,1 TERRY D. COPELAND,' STEPHEN OROSZLAN,1 AND JOHN F. EDWARDS2 Laboratory of Molecular Virology and Carcinogenesis, ABL-Basic Research Program, NCI-Frederick Cancer Research and Development Center, Frederick, Maryland 21701,1 and Department of Veterinary Pathology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 778432 Received 22 December 1989/Accepted 10 May 1990 Downloaded from The transmembrane (TM) envelope protein of lentiviruses, including equine infectious anemia virus (EIAV), is significantly larger than that of other retroviruses and may extend in the C-terminal direction 100 to 200 amino acids beyond the TM domain. This size difference suggests a lentivirus-specific function for the long C-terminal extension. We have investigated the synthesis and processing of the EIAV TM protein by immune precipitation and immunoblotting experiments, by using several envelope-specific peptide antisera. We show that the TM protein in EIAV particles is cleaved by proteolysis to an N-terminal glycosylated 32- to 35-kilodalton (kDa) segment and a C-terminal nonglycosylated 20-kDa segment. The 20-kDa fragment was isolated from virus fractionated by high-pressure liquid chromatography, and its N-terminal amino acid sequence was determined for 13 residues. Together with the known nucleotide sequence, this fixes the cleavage http://jvi.asm.org/ site at a His-Leu bond located 240 amino acids from the N terminus of the TM protein. -
Adaptive Evolution of the SIV Envelope Protein During Early SIV Infection
Adaptive Evolution of the SIV Envelope Protein During Early SIV Infection The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Ita, Sergio. 2016. Adaptive Evolution of the SIV Envelope Protein During Early SIV Infection. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493399 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Adaptive Evolution of the SIV Envelope Protein during Early SIV Infection A dissertation presented by Sergio Ita to The Division of Medical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Virology Harvard University Cambridge, Massachusetts January 2016 © 2016 Sergio Ita All rights reserved. Dissertation Advisor: Dr. Welkin E. Johnson Sergio Ita Adaptive Evolution of the SIV Envelope Protein during Early SIV infection Abstract Primate lentiviruses (PLVs), including human immunodeficiency virus type 1 (HIV-1), HIV type 2 (HIV-2), and the simian immunodeficiency viruses (SIVs), cause persistent lifelong infections despite the presence of virus-specific adaptive immune responses. The target of antibodies is the viral envelope glycoprotein (Env), which is expressed on the surface of virions and infected cells as a trimer of gp120:gp41 heterodimers. SIV env sequence variation arising from evasion of antibodies is well established and closely mimics the pattern observed in HIV-infected human patients, yet despite the experimental advantages of the macaque model, the viral dynamics during acute and early infection leading to escape within env have not been well defined. -
Educator Materials Hands-On Activity HIV Reverse Transcription and AZT
Hands-on Activity HIV Reverse Transcription and AZT Educator Materials HIV REVERSE TRANSCRIPTION AND AZT OVERVIEW This hands-on activity is part of a series of activities and demonstrations focusing on various aspects of the human immunodeficiency virus (HIV) life cycle. In this activity, students will model how the anti-HIV drug AZT (azidothymidine) interferes with the process of viral replication and reduces the amount of virus in the Body. Students will first model reverse transcription, the process that results in the production of a double- stranded DNA copy of the HIV single-stranded RNA genome. (See introduction in the student document for a review of the process.) Using an actual HIV RNA sequence as a template, students will model the synthesis of a complementary strand of DNA By attaching nucleotides to one another. Then, students will demonstrate AZT’s effect on this process. They will suBstitute AZT in place of thymidine. AZT lacks a hydroxyl (OH) group that is necessary for suBsequent nucleotides to attach. When AZT is incorporated in a growing DNA sequence it prevents further nucleotides from Being added, thereby blocking the production of HIV DNA. Following this activity, it may Be helpful for students to complete the HIV integration activity. LEARNING OBJECTIVES Students will Be able to: • Code DNA from RNA. • Demonstrate the process of reverse transcription. • Understand the role of the enzyme reverse transcriptase in the formation of viral DNA. • Review the chemical structures of nucleic acids and identify structural -
Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia. -
De Novo POGZ Mutations in Sporadic
Matsumura et al. Journal of Molecular Psychiatry (2016) 4:1 DOI 10.1186/s40303-016-0016-x SHORT REPORT Open Access De novo POGZ mutations in sporadic autism disrupt the DNA-binding activity of POGZ Kensuke Matsumura1, Takanobu Nakazawa2*, Kazuki Nagayasu2, Nanaka Gotoda-Nishimura1, Atsushi Kasai1, Atsuko Hayata-Takano1, Norihito Shintani1, Hidenaga Yamamori3, Yuka Yasuda3, Ryota Hashimoto3,4 and Hitoshi Hashimoto1,2,4 Abstract Background: A spontaneous de novo mutation is a new mutation appeared in a child that neither the parent carries. Recent studies suggest that recurrent de novo loss-of-function mutations identified in patients with sporadic autism spectrum disorder (ASD) play a key role in the etiology of the disorder. POGZ is one of the most recurrently mutated genes in ASD patients. Our laboratory and other groups have recently found that POGZ has at least 18 independent de novo possible loss-of-function mutations. Despite the apparent importance, these mutations have never previously been assessed via functional analysis. Methods: Using wild-type, the Q1042R-mutated, and R1008X-mutated POGZ, we performed DNA-binding experiments for proteins that used the CENP-B box sequence in vitro. Data were statistically analyzed by one-way ANOVA followed by Tukey-Kramer post hoc tests. Results: This study reveals that ASD-associated de novo mutations (Q1042R and R1008X) in the POGZ disrupt its DNA-binding activity. Conclusions: Here, we report the first functional characterization of de novo POGZ mutations identified in sporadic ASD cases. These findings provide important insights into the cellular basis of ASD. Keywords: Autism spectrum disorder, Recurrent mutation, De novo mutation, POGZ, DNA-binding activity Background including CHD8, ARID1B, SYNGAP1, DYRK1A, SCN2A, The genetic etiology of autism spectrum disorder (ASD) ANK2, ADNP, DSCAM, CHD2, KDM5B, SUV420H1, remains poorly understood. -
POGZ Gene Pogo Transposable Element Derived with ZNF Domain
POGZ gene pogo transposable element derived with ZNF domain Normal Function The POGZ gene provides instructions for making a protein that is found in the cell nucleus. The POGZ protein is part of a group known as zinc finger proteins, which contain one or more short regions called zinc finger domains. These regions include a specific pattern of protein building blocks (amino acids) and one or more charged atoms of zinc (zinc ions). The folded configuration of the zinc finger domain stabilizes the protein and allows it to attach (bind) to other molecules. In the cell nucleus, the POGZ protein attaches (binds) to chromatin, which is the network of DNA and proteins that packages DNA into chromosomes. Binding of the POGZ protein is part of the process that changes the structure of chromatin (chromatin remodeling) to alter how tightly regions of DNA are packaged. Chromatin remodeling is one way gene activity (expression) is regulated; when DNA is tightly packed gene expression is lower than when DNA is loosely packed. Regulation of gene expression by the POGZ protein is thought to be important to brain development, but the specific function of POGZ in the brain is not well understood. Health Conditions Related to Genetic Changes White-Sutton syndrome At least 17 POGZ gene mutations have been found to cause White-Sutton syndrome. This disorder is characterized by intellectual disability, specific facial features, and other signs and symptoms affecting various parts of the body, particularly vision problems and gastrointestinal problems. Most affected individuals have features of autism spectrum disorder (ASD), a varied condition characterized by impaired social skills, communication problems, and repetitive behaviors. -
The Function and Evolution of C2H2 Zinc Finger Proteins and Transposons
The function and evolution of C2H2 zinc finger proteins and transposons by Laura Francesca Campitelli A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Molecular Genetics University of Toronto © Copyright by Laura Francesca Campitelli 2020 The function and evolution of C2H2 zinc finger proteins and transposons Laura Francesca Campitelli Doctor of Philosophy Department of Molecular Genetics University of Toronto 2020 Abstract Transcription factors (TFs) confer specificity to transcriptional regulation by binding specific DNA sequences and ultimately affecting the ability of RNA polymerase to transcribe a locus. The C2H2 zinc finger proteins (C2H2 ZFPs) are a TF class with the unique ability to diversify their DNA-binding specificities in a short evolutionary time. C2H2 ZFPs comprise the largest class of TFs in Mammalian genomes, including nearly half of all Human TFs (747/1,639). Positive selection on the DNA-binding specificities of C2H2 ZFPs is explained by an evolutionary arms race with endogenous retroelements (EREs; copy-and-paste transposable elements), where the C2H2 ZFPs containing a KRAB repressor domain (KZFPs; 344/747 Human C2H2 ZFPs) are thought to diversify to bind new EREs and repress deleterious transposition events. However, evidence of the gain and loss of KZFP binding sites on the ERE sequence is sparse due to poor resolution of ERE sequence evolution, despite the recent publication of binding preferences for 242/344 Human KZFPs. The goal of my doctoral work has been to characterize the Human C2H2 ZFPs, with specific interest in their evolutionary history, functional diversity, and coevolution with LINE EREs. -
Proviruses with Long-Term Stable Expression Accumulate In
viruses Article Proviruses with Long-Term Stable Expression Accumulate in Transcriptionally Active Chromatin Close to the Gene Regulatory Elements: Comparison of ASLV-, HIV- and MLV-Derived Vectors Dalibor Miklík 1,2, Filip Šenigl 1 and Jiˇrí Hejnar 1,* 1 Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, CZ-14220 Prague 4, Czech Republic; [email protected] (D.M.); [email protected] (F.S.) 2 Faculty of Science, Charles University, Albertov 6, CZ-12843 Prague 2, Czech Republic * Correspondence: [email protected] Received: 29 January 2018; Accepted: 6 March 2018; Published: 8 March 2018 Abstract: Individual groups of retroviruses and retroviral vectors differ in their integration site preference and interaction with the host genome. Hence, immediately after infection genome-wide distribution of integrated proviruses is non-random. During long-term in vitro or persistent in vivo infection, the genomic position and chromatin environment of the provirus affects its transcriptional activity. Thus, a selection of long-term stably expressed proviruses and elimination of proviruses, which have been gradually silenced by epigenetic mechanisms, helps in the identification of genomic compartments permissive for proviral transcription. We compare here the extent and time course of provirus silencing in single cell clones of the K562 human myeloid lymphoblastoma cell line that have been infected with retroviral reporter vectors derived from avian sarcoma/leukosis virus (ASLV), human immunodeficiency virus type 1 (HIV) and murine leukaemia virus (MLV). While MLV proviruses remain transcriptionally active, ASLV proviruses are prone to rapid silencing. The HIV provirus displays gradual silencing only after an extended time period in culture. -
HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing Assay
crossmark HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing Assay Sara Sunshine,a Rory Kirchner,b Sami S. Amr,c Leandra Mansur,c Rimma Shakhbatyan,c Michelle Kim,d,e Alberto Bosque,f Robert F. Siliciano,d,e Vicente Planelles,f Oliver Hofmann,b Shannan Ho Sui,b Jonathan Z. Lia Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USAa; Bioinformatics Core, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USAb; Partners HealthCare Personalized Medicine, Cambridge, Massachusetts, USAc; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USAd; Howard Hughes Medical Institute, Chevy Chase, Maryland, USAe; Department of Pathology, University of Utah, Salt Lake City, Utah, USAf ABSTRACT Downloaded from Antiretroviral therapy (ART) is successful in the suppression of HIV but cannot target and eradicate the latent proviral reservoir. The location of retroviral integration into the human genome is thought to play a role in the clonal expansion of infected cells and HIV persistence. We developed a high-throughput targeted sequence capture assay that uses a pool of HIV-specific probes to enrich Illumina libraries prior to deep sequencing. Using an expanded clonal population of ACH-2 cells, we demonstrate that this sequence capture assay has an extremely low false-positive rate. This assay assessed four cellular models commonly used to -study HIV latency and latency-reversing agents: ACH-2 cells, J-Lat cells, the Bcl-2-transduced primary CD4؉ model, and the cul ؉ tured TCM (central memory) CD4 model. HIV integration site characteristics and genes were compared between these cellular models and to previously reported patient data sets.