DOCSLIB.ORG

The Tip60 Chromatin Remodeling Complex Is Required for Maintenance and Polarity of Drosophila Neural Stem Cells

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Tip60 Chromatin Remodeling Complex Is Required for Maintenance and Polarity of Drosophila Neural Stem Cells The Tip60 chromatin remodeling complex is required for maintenance and polarity of Drosophila neural stem cells Dissertation for the award of the degree “Doctor rerum naturalium” (Dr. rer. nat.) Division of Mathematics and Natural Sciences of the Georg-August-University Göttingen submitted by Katja Rust from Hanover Göttingen, 2016 Members of the Thesis Committee Prof. Dr. Andreas Wodarz Institute I of Anatomy (Referee and Thesis Supervisor) Department of Molecular Cell Biology University of Cologne Prof. Dr. Tomas Pieler University Medical Center (Co-Referee) Department of Developmental Biochemistry Georg-August-University, Göttingen PD Dr. Halyna Shcherbata Max Planck Institute for Biophysical Chemistry Gene Expression and Signaling Göttingen Further Members of the Examination Board Prof. Dr. Matthias Dobbelstein University Medical Center Institute for Molecular Oncology Georg-August-University, Göttingen Dr. Roland Dosch University Medical Center Deparment of Developmental Biochemistry Georg-August-University, Göttingen Prof. Dr. Ernst Wimmer Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology Department of Developmental Biology Georg-August-University, Göttingen Date of the oral examination: 18th November 2016 Affidavit Affidavit I hereby declare that I prepared the thesis “The Tip60 chromatin remodeling complex is required for maintenance and polarity of Drosophila neural stem cells” on my own and with no other sources and aids than quoted. Katja Rust Göttingen, September 30th, 2016 Table of contents Table of contents Abstract ....................................................................................................................... 1 1. Introduction .......................................................................................................... 3 1.1. Drosophila neurogenesis .................................................................................................. 3 1.1.1. The embryonic epithelium: Parent tissue of the Drosophila neuroblast ..................... 3 1.1.2. Neural stem cells in Drosophila development ............................................................. 6 1.1.3. Neuroblast polarity and asymmetric division .............................................................. 8 1.1.4. Drosophila neuroblasts terminate neurogenesis ....................................................... 12 1.2. Drosophila intestinal stem cells ...................................................................................... 13 1.3. The Tip60 chromatin remodeling complex ..................................................................... 15 1.3.1. Domino: A chromatin remodeler ATPase .................................................................. 19 1.3.2. Specific interactors define Tip60 complex functions ................................................. 23 1.4. The roles of the transcription factor Myc in stem cells .................................................. 30 1.5. Scope of the thesis .......................................................................................................... 32 2. Materials and Methods ....................................................................................... 33 2.1. Materials ......................................................................................................................... 33 2.1.1. Chemicals, enzymes and kits ...................................................................................... 33 2.1.2. Antibodies .................................................................................................................. 33 2.1.3. Fly stocks .................................................................................................................... 34 2.1.4. Oligonucleotides ........................................................................................................ 38 2.1.5. Vectors ....................................................................................................................... 38 2.1.6. Bacterial strains .......................................................................................................... 38 2.1.7. Buffer and reagent recipes......................................................................................... 39 2.1.8. Microscope and imaging systems .............................................................................. 46 2.1.9. Other systems ............................................................................................................ 47 2.1.10. Software ..................................................................................................................... 47 2.2. Methods .......................................................................................................................... 47 2.2.1. Molecular biology methods ....................................................................................... 47 2.2.2. Biochemical methods ................................................................................................. 52 2.2.3. Histology and cell culture ........................................................................................... 54 2.2.4. Fly work .................................................................................................................... 60 2.2.5. Statistical analysis ...................................................................................................... 61 2.2.6. Next generation sequencing ...................................................................................... 62 3. Results ................................................................................................................ 64 3.1. Domino is required for Drosophila embryonic development ......................................... 64 3.1.1. Domino is expressed ubiquitously during oogenesis and embryogenesis ................ 64 3.1.2. Neuroblasts in domino null mutants are misoriented ............................................... 69 3.1.3. Embryonic epithelial morphology is disturbed in domino mutants........................... 72 3.1.4. domino mutation leads to nuclear fragmentation..................................................... 77 3.1.5. domino mutation does not induce apoptosis in the Drosophila embryo .................. 78 3.2. Domino controls Drosophila imaginal disc development ............................................... 80 3.3. Domino and the Tip60 complex regulate larval neuroblast division .............................. 84 3.3.1. Domino is expressed in the larval central brain ......................................................... 84 3.3.2. Domino and the Tip60 complex are required for neural cell lineages ...................... 86 3.3.3. Lack of neuroblasts upon domino knockdown is independent of apoptosis ............ 97 3.3.4. domino knockdown leads to polarity defects in larval neuroblasts .......................... 98 Table of contents 3.3.5. domino deficient larval neuroblasts display features of termination of neurogenesis ............................................................................................................ 101 3.3.6. Neuroblast division and its asymmetry is disturbed upon domino knockdown ...... 106 3.4. Myc interacts with the Tip60 complex to maintain larval neuroblasts ........................ 109 3.4.1. Identification of potential Domino interactors in the maintenance of Drosophila larval neuroblasts ..................................................................................................... 109 3.4.2. myc depleted neuroblasts exhibit polarity defects and resemble neuroblasts undergoing terminal differentiation ........................................................................ 113 3.4.3. Myc interacts genetically with the Tip60 complex in larval neuroblasts ................. 115 3.4.4. Tip60 histone substrates in larval neuroblasts ........................................................ 118 3.5. Overexpression of single components of the Myc/Tip60 network does not maintain neuroblasts ................................................................................................................... 119 3.6. Domino regulates the expression of a large set of target genes .................................. 121 3.6.1. Domino target genes regulate neuroblast fate ........................................................ 127 3.7. Domino maintains adult midgut precursors ................................................................. 128 4. Discussion ......................................................................................................... 131 4.1. Domino acts in the Tip60 complex to maintain Drosophila neural stem cells ............. 131 4.2. The Tip60 complex interacts with Myc to regulate neuroblast self-renewal ............... 133 4.2.1. Myc and the Tip60 complex potentially interact to regulate gene expression in larval neuroblasts ..................................................................................................... 134 4.2.2. The Tip60 complex and Myc preserve neuroblast polarity and inhibit premature differentiation .......................................................................................................... 139 4.2.3. Links between the Myc/Tip60 network and neuroblast division ............................. 146 4.2.4. The Myc/Tip60 pathway: A general key player of stem cell maintenance? ............ 147 4.3. Domino is potentially required for various processes in Drosophila development ..... 149 5. Conclusion
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Multiple Cellular Proteins Interact with LEDGF/P75 Through a Conserved Unstructured Consensus Motif
    ARTICLE Received 19 Jan 2015 | Accepted 1 Jul 2015 | Published 6 Aug 2015 DOI: 10.1038/ncomms8968 Multiple cellular proteins interact with LEDGF/p75 through a conserved unstructured consensus motif Petr Tesina1,2,3,*, Katerˇina Cˇerma´kova´4,*, Magdalena Horˇejsˇ´ı3, Katerˇina Procha´zkova´1, Milan Fa´bry3, Subhalakshmi Sharma4, Frauke Christ4, Jonas Demeulemeester4, Zeger Debyser4, Jan De Rijck4,**, Va´clav Veverka1,** & Pavlı´na Rˇeza´cˇova´1,3,** Lens epithelium-derived growth factor (LEDGF/p75) is an epigenetic reader and attractive therapeutic target involved in HIV integration and the development of mixed lineage leukaemia (MLL1) fusion-driven leukaemia. Besides HIV integrase and the MLL1-menin complex, LEDGF/p75 interacts with various cellular proteins via its integrase binding domain (IBD). Here we present structural characterization of IBD interactions with transcriptional repressor JPO2 and domesticated transposase PogZ, and show that the PogZ interaction is nearly identical to the interaction of LEDGF/p75 with MLL1. The interaction with the IBD is maintained by an intrinsically disordered IBD-binding motif (IBM) common to all known cellular partners of LEDGF/p75. In addition, based on IBM conservation, we identify and validate IWS1 as a novel LEDGF/p75 interaction partner. Our results also reveal how HIV integrase efficiently displaces cellular binding partners from LEDGF/p75. Finally, the similar binding modes of LEDGF/p75 interaction partners represent a new challenge for the development of selective interaction inhibitors. 1 Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo nam. 2, 166 10 Prague, Czech Republic. 2 Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 128 44 Prague, Czech Republic.
    [Show full text]
  • How Influenza Virus Uses Host Cell Pathways During Uncoating
    cells Review How Influenza Virus Uses Host Cell Pathways during Uncoating Etori Aguiar Moreira 1 , Yohei Yamauchi 2 and Patrick Matthias 1,3,* 1 Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; [email protected] 2 Faculty of Life Sciences, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; [email protected] 3 Faculty of Sciences, University of Basel, 4031 Basel, Switzerland * Correspondence: [email protected] Abstract: Influenza is a zoonotic respiratory disease of major public health interest due to its pan- demic potential, and a threat to animals and the human population. The influenza A virus genome consists of eight single-stranded RNA segments sequestered within a protein capsid and a lipid bilayer envelope. During host cell entry, cellular cues contribute to viral conformational changes that promote critical events such as fusion with late endosomes, capsid uncoating and viral genome release into the cytosol. In this focused review, we concisely describe the virus infection cycle and highlight the recent findings of host cell pathways and cytosolic proteins that assist influenza uncoating during host cell entry. Keywords: influenza; capsid uncoating; HDAC6; ubiquitin; EPS8; TNPO1; pandemic; M1; virus– host interaction Citation: Moreira, E.A.; Yamauchi, Y.; Matthias, P. How Influenza Virus Uses Host Cell Pathways during 1. Introduction Uncoating. Cells 2021, 10, 1722. Viruses are microscopic parasites that, unable to self-replicate, subvert a host cell https://doi.org/10.3390/ for their replication and propagation. Despite their apparent simplicity, they can cause cells10071722 severe diseases and even pose pandemic threats [1–3].
    [Show full text]
  • Characterization of the Relationship Between Measles Virus Fusion
    University of Massachusetts Medical School eScholarship@UMMS GSBS Dissertations and Theses Graduate School of Biomedical Sciences 2006-05-17 Characterization of the Relationship Between Measles Virus Fusion, Receptor Binding, and the Virus-Specific Interaction Between the Hemagglutinin and Fusion Glycoproteins: a Dissertation Elizabeth Ann Corey University of Massachusetts Medical School Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/gsbs_diss Part of the Amino Acids, Peptides, and Proteins Commons, Cells Commons, Chemical Actions and Uses Commons, Lipids Commons, and the Virus Diseases Commons Repository Citation Corey EA. (2006). Characterization of the Relationship Between Measles Virus Fusion, Receptor Binding, and the Virus-Specific Interaction Between the Hemagglutinin and Fusion Glycoproteins: a Dissertation. GSBS Dissertations and Theses. https://doi.org/10.13028/hg2y-0r35. Retrieved from https://escholarship.umassmed.edu/gsbs_diss/221 This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in GSBS Dissertations and Theses by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. CHARACTERIZATION OF THE RELATIONSHIP BETWEEN MEASLES VIRUS FUSION , RECEPTOR BINDING , AND THE VIRUS-SPECIFIC INTERACTION BETWEEN THE HEMAGGLUTININ AND FUSION GL YCOPROTEINS A Dissertation Presented Elizabeth Anne Corey Submitted to the Faculty of the University of Massachusetts Graduate
    [Show full text]
  • Rotavirus Contains Integrin Ligand Sequences and a Disintegrin-Like Domain That Are Implicated in Virus Entry Into Cells
    Proc. Natl. Acad. Sci. USA Vol. 94, pp. 5389–5394, May 1997 Microbiology Rotavirus contains integrin ligand sequences and a disintegrin-like domain that are implicated in virus entry into cells BARBARA S. COULSON†,SARAH L. LONDRIGAN, AND DEBRA J. LEE Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3052, Australia Communicated by Wolfgang K. Joklik, Duke University Medical Center, Durham, NC, March 13, 1997 (received for review January 3, 1997) ABSTRACT Rotavirus contains two outer capsid viral binding and infectivity of rhesusymurine and simianyhuman proteins, the spike protein VP4 and major capsid component virus reassortants differing in their requirements for cellular VP7, both of which are implicated in cell entry. We show that sialic acid correlated with the parental origin of gene 4 (11). VP4 and VP7 contain tripeptide sequences previously shown Earlier studies implicated VP7 as a rotavirus cell attachment to act as recognition sites for integrins in extracellular matrix protein. Two laboratories reported that a protein in infected proteins. VP4 contains the a2b1 integrin ligand site DGE. In cell lysates identified as VP7 by antiserum blocking and VP7, the axb2 integrin ligand site GPR and the a4b1 integrin adsorption with mAbs bound to MA104 cell monolayers (2, ligand site LDV are embedded in a novel disintegrin-like 12). It was later suggested that this protein was the nonstruc- domain that also shows sequence similarity to fibronectin and tural protein NSP2, rather than VP7 (13). It remains possible the tie receptor tyrosine kinase. Microorganism sequence that VP7 has a minor role in cell attachment (11). homology to these ligand motifs and to disintegrins has not Rotavirus infection of cells appears to be a multi-step been reported previously.
    [Show full text]
  • HIV-1) CD4 Receptor and Its Central Role in Promotion of HIV-1 Infection
    MICROBIOLOGICAL REVIEWS, Mar. 1995, p. 63–93 Vol. 59, No. 1 0146-0749/95/$04.0010 Copyright q 1995, American Society for Microbiology The Human Immunodeficiency Virus Type 1 (HIV-1) CD4 Receptor and Its Central Role in Promotion of HIV-1 Infection STEPHANE BOUR,* ROMAS GELEZIUNAS,† AND MARK A. WAINBERG* McGill AIDS Centre, Lady Davis Institute-Jewish General Hospital, and Departments of Microbiology and Medicine, McGill University, Montreal, Quebec, Canada H3T 1E2 INTRODUCTION .........................................................................................................................................................63 RETROVIRAL RECEPTORS .....................................................................................................................................64 Receptors for Animal Retroviruses ........................................................................................................................64 CD4 Is the Major Receptor for HIV-1 Infection..................................................................................................65 ROLE OF THE CD4 CORECEPTOR IN T-CELL ACTIVATION........................................................................65 Structural Features of the CD4 Coreceptor..........................................................................................................65 Interactions of CD4 with Class II MHC Determinants ......................................................................................66 CD4–T-Cell Receptor Interactions during T-Cell Activation
    [Show full text]
  • Analysis of the Dark Proteome of Chandipura Virus Reveals Maximum Propensity for Intrinsic Disorder in Phosphoprotein Nishi R
    www.nature.com/scientificreports OPEN Analysis of the dark proteome of Chandipura virus reveals maximum propensity for intrinsic disorder in phosphoprotein Nishi R. Sharma1*, Kundlik Gadhave2, Prateek Kumar2, Mohammad Saif1, Md. M. Khan1, Debi P. Sarkar3, Vladimir N. Uversky4,5* & Rajanish Giri2* Chandipura virus (CHPV, a member of the Rhabdoviridae family) is an emerging pathogen that causes rapidly progressing infuenza-like illness and acute encephalitis often leading to coma and death of the human host. Given several CHPV outbreaks in Indian sub-continent, recurring sporadic cases, neurological manifestation, and high mortality rate of this infection, CHPV is gaining global attention. The ‘dark proteome’ includes the whole proteome with special emphasis on intrinsically disordered proteins (IDP) and IDP regions (IDPR), which are proteins or protein regions that lack unique (or ordered) three-dimensional structures within the cellular milieu. These proteins/regions, however, play a number of vital roles in various biological processes, such as cell cycle regulation, control of signaling pathways, etc. and, therefore, are implicated in many human diseases. IDPs and IPPRs are also abundantly found in many viral proteins enabling their multifunctional roles in the viral life cycles and their capability to highjack various host systems. The unknown abundance of IDP and IDPR in CHPV, therefore, prompted us to analyze the dark proteome of this virus. Our analysis revealed a varying degree of disorder in all fve CHPV proteins, with the maximum level of intrinsic disorder propensity being found in Phosphoprotein (P). We have also shown the fexibility of P protein using extensive molecular dynamics simulations up to 500 ns (ns).
    [Show full text]
  • Phosphorylation Cascade Regulates the Formation and Maturation of Rotaviral Replication Factories
    Phosphorylation cascade regulates the formation and maturation of rotaviral replication factories Jeanette M. Criglara,1, Ramakrishnan Anishb,1, Liya Hub, Sue E. Crawforda, Banumathi Sankaranc, B. V. Venkataram Prasada,b, and Mary K. Estesa,d,2 aDepartment of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030; bVerna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030; cMolecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and dDepartment of Medicine, Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX 77030 Contributed by Mary K. Estes, October 19, 2018 (sent for review October 13, 2017; reviewed by Oscar R. Burrone and Ulrich Desselberger) The rotavirus (RV) genome is replicated and packaged into virus interact are available, exactly how these two proteins initiate progeny in cytoplasmic inclusions called viroplasms, which require viroplasm formation remains unclear (10–12). interactions between RV nonstructural proteins NSP2 and NSP5. NSP2, a 35-kDa monomer, forms octamers in solution and has How viroplasms form remains unknown. We previously found two several enzymatic activities, including nucleoside-triphosphatase forms of NSP2 in RV-infected cells: a cytoplasmically dispersed (NTPase), 5′-RNA triphosphatase (RTPase), and nucleoside- dNSP2, which interacts with hypophosphorylated NSP5; and a diphosphate (NDP) kinase-like activities (13–15). We previously viroplasm-specific vNSP2, which interacts with hyperphosphory- reported the identification of two distinct forms of NSP2 that lated NSP5. Other studies report that CK1α, a ubiquitous cellular differ in temporal appearance and conformation in RV-infected kinase, hyperphosphorylates NSP5, but requires NSP2 for reasons cells (16).
    [Show full text]