RNA-Dependent RNA Polymerase Consensus Sequence of the L-A Double-Stranded RNA Virus: Definition of Essential Domains

Total Page:16

File Type:pdf, Size:1020Kb

RNA-Dependent RNA Polymerase Consensus Sequence of the L-A Double-Stranded RNA Virus: Definition of Essential Domains Proc. Nati. Acad. Sci. USA Vol. 89, pp. 2185-2189, March 1992 Biochemistry RNA-dependent RNA polymerase consensus sequence of the L-A double-stranded RNA virus: Definition of essential domains JUAN CARLOS RIBAS AND REED B. WICKNER Section on the Genetics of Simple Eukaryotes, Laboratory of Biochemical Pharmacology, National Institute of Diabetes and Digestive and Kidney Diseases, Building 8, Room 207, National Institutes of Health, Bethesda, MD 20892 Communicated by Herbert Tabor, November 27, 1991 (received for review October 2, 1991) ABSTRACT The L-A double-stranded RNA virus of Sac- lacking M1 (reviewed in refs. 10 and 18). M1 depends on L-A charomyces cerevisiac makes a gag-pol fusion protein by a -1 for its coat and replication proteins (19). MAK10 is one of ribosomal frameshift. The pol amino acid sequence includes three chromosomal genes needed for L-A virus propagation consensus patterns typical of the RNA-dependent RNA poly- within yeast cells (20). In a maklO host, L-A proteins merases (EC 2.7.7.48) of (+) strand and double-stranded RNA expressed from a cDNA clone of L-A support the replication viruses of animals and plants. We have carried out "alanine- of the M1 satellite virus but (for unknown reasons) do not scanning mutagenesis" of the region of L-A including the two support propagation of the L-A virus itself (21). Thus, while most conserved polymerase motifs, SG...T...NT..N (. = any L-A requires the MAK10 product itself, M1 requires MAK10 amino acid) and GDD. By constructing and analyzing 46 only because it requires the L-A-encoded proteins. We have different mutations in and around the RNA polymerase con- used this phenomenon to assay the importance for viral sensus regions, we have precisely dermed the extent of domains propagation of specific sequences encoded by L-A. Previous and specific residues essential for viral replication. Assuming work to examine the importance of the amino acid patterns that this highly conserved region has a common secondary conserved among RNA-dependent RNA polymerases has structure among different viruses, we predict a largely fl-sheet dealt with the enzymes encoded by Qf phage, poliovirus, and structure. brome mosaic virus (22-24). We have defined the regions surrounding the two most The (+) strand RNA viruses of animals and plants share highly conserved RNA polymerase consensus patterns that amino acid sequence patterns in their RNA-dependent RNA are necessary for viral propagation. We show that, although polymerase (EC 2.7.7.48) regions (1-3) (Fig. 1). The same these domains are highly conserved among a broad range of patterns are present in most of the dsRNA viruses whose viruses in both primary structure and predicted secondary polymerase segment has been sequenced, including the L-A structure, they are not interchangeable. virus of Saccharomyces cerevisiae (4), reovirus (5), blue- tongue virus (6), and rotavirus (7). Two other dsRNA viruses MATERIALS AND METHODS [46 phage (8) and infectious bursal disease virus (9)] show a less clear fit to the pattern. The extent of these common Strains and Media. YPAD, YPG, 4.7MB, SD, and synthetic sequence patterns suggests that there is a common structure complete medium (25) and LB medium (26) have been and function among the more than 50 viral enzymes for which described. S. cerevisiae strains 2955p0 (MATa trpl adel his3 sequence data are available and that information obtained maklO-1 L-A-o M-o p0), 2629 (MATa leul karl-i L-A-HNB about one of them may be applicable to others. While M1), and 5X47 (MATa/MATa hisl /+ trpl/+ ura3/+ [KIL- different enzymes must recognize different sites on viral o]) were used. DNA sequencing was done by the dideoxy RNA and interact with different viral and host proteins, there method of Sanger et al. (27) with deoxyadenosine 5'-[a- are also common functions which they must carry out, [35S]thio]triphosphate, using a Sequenase kit [United States including binding of Mg2' and rNTPs, holding onto the Biochemical (28)]. template RNA chain, and the chain elongation reaction itself. Site-Directed Mutagenesis. Mutagenesis of the L-A cDNA It is likely that these conserved sequence patterns are part of expression plasmid pI2L2 (21) was carried out as described domains responsible for such common functions. by Kunkel (29), using the Muta-Gene kit from Bio-Rad. All The L-A dsRNA virus ofyeast replicates by a conservative mutations were confirmed by sequencing. To ensure that loss mechanism with (+) and (-) strands made inside the viral of activity was due to the introduced mutation and not to particle at different points in the replication cycle (reviewed changes elsewhere in the L-A sequence or vector, two or in ref. 10). In vitro systems for replication, transcription, and three mutants were checked for each change, and 16 wild- packaging are available, and the signals for the replication type clones (nonmutant at the site where mutagenesis was step and for packaging have been defined (11-14). L-A attempted) isolated during attempts to make mutations were encodes its 70-kDa major coat protein (called gag) (4, 15) and tested. All mutants of a given type were either all inactive or a 170-kDa gag-pol fusion protein (4, 16) formed by a -1 all active, and all ofthe wild-type clones isolated were active. ribosomal frameshift indistinguishable in mechanism from This approach may be ofgeneral utility in extensive localized that used by retroviruses for a similar purpose (17). The pol mutagenesis projects when complete resequencing of each region of the gag-pol fusion protein (4) has all the character- mutant isolate or insertion of mutagenized segments into istic sequence patterns identified by Kamer and Argos (1) as unmutagenized vectors would be impractical. typical of (+) strand RNA viral RNA-dependent RNA poly- Substitution of Homologous Domains of Other Viruses by merases. Asymmetric PCR. Fragments of 81, 105, and 225 nucleotides The M1 satellite virus of L-A encodes a protein, the killer from reovirus segment Li (5) and of 87, 159, and 180 toxin, that is secreted by cells carrying M1 and kills cells nucleotides from Sindbis virus (30) were amplified in a PCR process as described (31), in two steps using the Gene Amp The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" Abbreviations: ssRNA and dsRNA, single-stranded and double- in accordance with 18 U.S.C. §1734 solely to indicate this fact. stranded RNA; ORF, open reading frame; aa, amino acids. 2185 Downloaded by guest on September 24, 2021 2186 Biochemistry: Ribas and Wickner Proc. Natl. Acad. Sci. USA 89 (1992) + Strand RNA Viruses: Carnat 524 GCRNMDNNALGNCLLACLITKH.............. LIKIRSRLINNflRCVLI TobEch 2580 KGNNEQPSXVVDIMNVIIAMLY .... .... TCEKCGINKEEIVYYVNMDDLLIA BromMV 521 FQR~fDAFYFG=LVTNAMIAY ............ ASDLSDCDCAIFSGDSLII TobMV 1440 YQRPEfDVTTFIGVIIAACLAS ....NI........K IKGAFcGfClSLLY Al fal faMV585 FQRM=DALZYAWUIVTLACLCH .... ........ VYDLMDPNFVVASMSLIG CowpeaMV1492 CGIPEFP !IVHIFNEILIRYHYK. 9 aa. ELNVQSFDKLIGLVTYgIDNLIS FIG. 1. Consensus sequence patterns ofviral RNA- dependent RNA polymerases of (+) single-stranded Mdlbrg 804 AMNKKW4FLILFVML3F4IAS .... ...... RVLEERLTNSKCAAFIERRNIVH RNA (ssRNA) viruses (1, 3) and double-stranded RNA WNileF 3120 DQRGMQVVTYALIFTNIAVQKV.25 aa.RTWLFENGEERLSRMAVSgRRCVVK YellowF 3100 DQRGDIQVVXYALifITNLKVQLI.25 aa.EAWLTEHGCDRLKRNAVSfRCVVR (dsRNA) viruses (4-9). The region shown here has the SINDBIS 2327 AMKKMXFLTLFVZVUVVIASRVL .......... EERLKTSRCAAFIMflRNIIH most extensive homology among these proteins, but DengueV 3088 DQRGEQVG!YGLMFTNEUAQLIRQ. 23 aa.WLARVGRERLSRNAISfIRRCVVK conserved patterns extend well beyond these in both N-terminal and C-terminal directions (1, 3). The most FootMDV 2156 GGMPflSCSATSII=ILNINIYVLYAL ...... RRHYEGVELDTYTNISYRIVVA EMC 2121 GGLICAATSNIflIMNNIIIRAGLY ...... LTYKNFEFDDVKVLSYflRLLVA highly conserved residues are shown by asterisks. The Rhinol4 2006 GGMPECSGXSIFIXINNIIIRT ..... LILDAYKGIDLD. KLKILAYflRLIVS viral sequences shown here are not more homologous Hepat A 1191 GSMPMfSPC!AILMIIPNVNLYY... VFSKIFGKSPVFFCQALKILCY MVLIF to L-A than those of other (+) ssRNA and dsRNA Polio 2025 GGNPM2CSGZSIFNMNINNLIIRT ..... LLLKTYKGIDLD.HLKMIAYgRVIAS viruses. Carnat, carnation mottle virus; TobEch, to- Coxsac B 300 GGMPIfCSGZSIFIMMINNIIIRT..... LMLKVYKGIDLD.QFRMIAYEDDVIAS bacco etch virus; MV, mosaic virus; TobMV, tobacco dURNA Viruses: mosaic virus; Mdlbrg, Middleburg virus; F, fever virus; L-A 544 GTLLQWRLTTFMtVLNWAYMKLAGV .......... FDLDDVQDSVHNflDVMIS FootMDV, foot-and-mouth disease virus; EMC, en- BTV 715 DTHILENSZLIANIMHXNAIGTLIQRA.... VGREQPGILTFLSEQYVMUfTLFY cephalomyocarditis; BTV, bluetongue virus; IBDV, ROTA V 586 GAVAMEKQZKAA]gIAXLULIKTVLSRISN ...... KYSFATKIIRVDgBMYAV REOVIRUS 676 TTFPSSTAZSTEUANNSTMMETFLTV... 20 aa . QRNYVCQOfWiGLMI infectious bursal disease virus; aa, amino acids. Amino PHI6 390 VGLSMQGAZDlIMg!LLSITYLVMQLD.24 aa.... QGHEEIRQISKARAILG acid symbols shown in lowercase do not agree with the IBDV 476 YGQGUNAA!FINULIETLVLDQWNL... 20 aa . NFKIERSIDDIRGK consensus. kit (Perkin-Elmer/Cetus). The first reaction mixture con- an in vivo assay ofthe activity ofthe proteins encoded by the tained 100 mM Tris HCI at pH 8.3, 50 mM KCl, 1.5 mM L-A cDNA clone in the absence of the L-A virus itself. The MgCl2, 0.001% gelatin, each dNTP at 0.2 mM, 2.5 units of stable maintenance of M1 by the L-A cDNA clone requires Taq DNA polymerase, 10-4 pmol of CsCl-purified DNA of both the major coat protein
Recommended publications
  • The Viruses of Vervet Monkeys and of Baboons in South Africa
    THE VIRUSES OF VERVET MONKEYS AND OF BABOONS IN SOUTH AFRICA Hubert Henri Malherbe A Thesis Submitted to the Faculty of Medicine University of the Witwatersrand, Johannesburg for the Degree of Doctor of Medicine Johannesburg 1974 11 ABSTRACT In this thesis are presented briefly the results of studies extending over the period 1955 to 1974. The use of vervet monkeys in South Africa for the production and testing of poliomyelitis vaccine made acquaintance with their viruses inevitable; and the subsequent introduction of the baboon as a laboratory animal of major importance also necessitates a knowledge of its viral flora. Since 1934 when Sabin and Wright described the B Virus which was recovered from a fatal human infection contracted as the result of a macaque monkey bite, numerous viral agents have been isolated from monkeys and baboons. In the United States of America, Dr. Robert N. Hull initiated the classification of simian viruses in an SV (for Simian Virus) series according to cytopathic effects as seen in unstained infected tissue cultures. In South Africa, viruses recovered from monkeys and baboons were designated numerically in an SA (for Simian Agent) series on the basis of cytopathic changes seen in stained preparations of infected cells. Integration of these two series is in progress. Simian viruses in South Africa have been recovered mainly through the inoculation of tissue cultures with material obtained by means of throat and rectal swabs, and also through the unmasking of latent agents present in kidney cells prepared as tissue cultures. Some evidence concerning viral activity has been derived from serological tests.
    [Show full text]
  • The Bunyaviridae Family, Has a Segmented RNA Genome with Negative Polarity
    Ludwig Institute for Cancer Research, Stockholm Branch and Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden Uukuniemi virus-like particles: a model system for bunyaviral assembly Anna K Överby Stockholm 2007 Anna K Överby Previously published papers were reproduced with permission from the publishers. Published and printed by Larserics digital print AB Box 20082, SE-161 02 Bromma, Sweden © Anna K Överby, 2007 ISBN 978-91-7357-238-5 To my wonderful parents Ge mej kraft att förändra det jag kan Tålamod att acceptera det jag inte kan förändra Och vishet att se skillnaden Carolines klokbok Anna K Överby Skapande består av en massa försök Populärvetenskaplig sammanfattning Populärvetenskaplig sammanfattning Alla levande organismer vi ser omkring oss är uppbyggda av celler. Det finns i stort sett två olika sorter, eukaryota (t.ex. djur och växtceller) och prokaryota (t.ex. bakterieceller) celler. Virus är inga celler utan små parasiter som lever inuti andra celler, både eukaryota och bakterieceller. Det finns en mängd olika virus som har grupperats in i familjer. Virus inom samma familj delar egenskaper såsom storlek och arvsegenskaper. Olika virus har genom åren specialiserat sig på att infektera och leva i olika celler och organismer. Vissa virus är så specialiserade att de bara kan infektera en speciell art. Poliovirus kan t.ex. endast infektera människor och apor. Man kan då utrota viruset genom att vaccinera hela jordens befolkning. Andra virus såsom Influensavirus kan infektera många olika arter t.ex. människa, fågel och gris. Vissa arter utvecklar ingen sjukdom och sprider bara viruset vidare medan andra orsakar akut sjukdom.
    [Show full text]
  • Sindbis Virus Infection in Resident Birds, Migratory Birds, and Humans, Finland Satu Kurkela,*† Osmo Rätti,‡ Eili Huhtamo,* Nathalie Y
    Sindbis Virus Infection in Resident Birds, Migratory Birds, and Humans, Finland Satu Kurkela,*† Osmo Rätti,‡ Eili Huhtamo,* Nathalie Y. Uzcátegui,* J. Pekka Nuorti,§ Juha Laakkonen,*¶ Tytti Manni,* Pekka Helle,# Antti Vaheri,*† and Olli Vapalahti*†** Sindbis virus (SINV), a mosquito-borne virus that (the Americas). SINV seropositivity in humans has been causes rash and arthritis, has been causing outbreaks in reported in various areas, and antibodies to SINV have also humans every seventh year in northern Europe. To gain a been found from various bird (3–5) and mammal (6,7) spe- better understanding of SINV epidemiology in Finland, we cies. The virus has been isolated from several mosquito searched for SINV antibodies in 621 resident grouse, whose species, frogs (8), reed warblers (9), bats (10), ticks (11), population declines have coincided with human SINV out- and humans (12–14). breaks, and in 836 migratory birds. We used hemagglutina- tion-inhibition and neutralization tests for the bird samples Despite the wide distribution of SINV, symptomatic and enzyme immunoassays and hemagglutination-inhibition infections in humans have been reported in only a few for the human samples. SINV antibodies were fi rst found in geographically restricted areas, such as northern Europe, 3 birds (red-backed shrike, robin, song thrush) during their and occasionally in South Africa (12), Australia (15–18), spring migration to northern Europe. Of the grouse, 27.4% and China (13). In the early 1980s in Finland, serologic were seropositive in 2003 (1 year after a human outbreak), evidence associated SINV with rash and arthritis, known but only 1.4% were seropositive in 2004.
    [Show full text]
  • Sindbis Virus Infection in Non-Blood-Fed Hibernating Culex Pipiens Mosquitoes in Sweden
    viruses Article Sindbis Virus Infection in Non-Blood-Fed Hibernating Culex pipiens Mosquitoes in Sweden Alexander Bergman, Emma Dahl, Åke Lundkvist and Jenny C. Hesson * Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, SE-751 23 Uppsala, Sweden; [email protected] (A.B.); [email protected] (E.D.); [email protected] (Å.L.) * Correspondence: [email protected] Academic Editors: Jonas Schmidt-Chanasit and Hanna Jöst Received: 19 November 2020; Accepted: 11 December 2020; Published: 14 December 2020 Abstract: A crucial, but unresolved question concerning mosquito-borne virus transmission is how these viruses can remain endemic in regions where the transmission is halted for long periods of time, due to mosquito inactivity in, e.g., winter. In northern Europe, Sindbis virus (SINV) (genus alphavirus, Togaviridae) is transmitted among birds by Culex mosquitoes during the summer, with occasional symptomatic infections occurring in humans. In winter 2018–19, we sampled hibernating Culex spp females in a SINV endemic region in Sweden and assessed them individually for SINV infection status, blood-feeding status, and species. The results showed that 35 out of the 767 collected mosquitoes were infected by SINV, i.e., an infection rate of 4.6%. The vast majority of the collected mosquitoes had not previously blood-fed (98.4%) and were of the species Cx. pipiens (99.5%). This is the first study of SINV overwintering, and it concludes that SINV can be commonly found in the hibernating Cx. pipiens population in an endemic region in Sweden, and that these mosquitoes become infected through other means besides blood-feeding.
    [Show full text]
  • A Novel Ebola Virus VP40 Matrix Protein-Based Screening for Identification of Novel Candidate Medical Countermeasures
    viruses Communication A Novel Ebola Virus VP40 Matrix Protein-Based Screening for Identification of Novel Candidate Medical Countermeasures Ryan P. Bennett 1,† , Courtney L. Finch 2,† , Elena N. Postnikova 2 , Ryan A. Stewart 1, Yingyun Cai 2 , Shuiqing Yu 2 , Janie Liang 2, Julie Dyall 2 , Jason D. Salter 1 , Harold C. Smith 1,* and Jens H. Kuhn 2,* 1 OyaGen, Inc., 77 Ridgeland Road, Rochester, NY 14623, USA; [email protected] (R.P.B.); [email protected] (R.A.S.); [email protected] (J.D.S.) 2 NIH/NIAID/DCR/Integrated Research Facility at Fort Detrick (IRF-Frederick), Frederick, MD 21702, USA; courtney.fi[email protected] (C.L.F.); [email protected] (E.N.P.); [email protected] (Y.C.); [email protected] (S.Y.); [email protected] (J.L.); [email protected] (J.D.) * Correspondence: [email protected] (H.C.S.); [email protected] (J.H.K.); Tel.: +1-585-697-4351 (H.C.S.); +1-301-631-7245 (J.H.K.) † These authors contributed equally to this work. Abstract: Filoviruses, such as Ebola virus and Marburg virus, are of significant human health concern. From 2013 to 2016, Ebola virus caused 11,323 fatalities in Western Africa. Since 2018, two Ebola virus disease outbreaks in the Democratic Republic of the Congo resulted in 2354 fatalities. Although there is progress in medical countermeasure (MCM) development (in particular, vaccines and antibody- based therapeutics), the need for efficacious small-molecule therapeutics remains unmet. Here we describe a novel high-throughput screening assay to identify inhibitors of Ebola virus VP40 matrix protein association with viral particle assembly sites on the interior of the host cell plasma membrane.
    [Show full text]
  • Cellular and Molecular Aspects of Rhabdovirus Interactions with Insect and Plant Hosts∗
    ANRV363-EN54-23 ARI 23 October 2008 14:4 Cellular and Molecular Aspects of Rhabdovirus Interactions with Insect and Plant Hosts∗ El-Desouky Ammar,1 Chi-Wei Tsai,3 Anna E. Whitfield,4 Margaret G. Redinbaugh,2 and Saskia A. Hogenhout5 1Department of Entomology, 2USDA-ARS, Department of Plant Pathology, The Ohio State University-OARDC, Wooster, Ohio 44691; email: [email protected], [email protected] 3Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720; email: [email protected] 4Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506; email: [email protected] 5Department of Disease and Stress Biology, The John Innes Centre, Norwich, NR4 7UH, United Kingdom; email: [email protected] Annu. Rev. Entomol. 2009. 54:447–68 Key Words First published online as a Review in Advance on Cytorhabdovirus, Nucleorhabdovirus, insect vectors, virus-host September 15, 2008 interactions, transmission barriers, propagative transmission The Annual Review of Entomology is online at ento.annualreviews.org Abstract This article’s doi: The rhabdoviruses form a large family (Rhabdoviridae) whose host ranges 10.1146/annurev.ento.54.110807.090454 include humans, other vertebrates, invertebrates, and plants. There are Copyright c 2009 by Annual Reviews. at least 90 plant-infecting rhabdoviruses, several of which are economi- by U.S. Department of Agriculture on 12/31/08. For personal use only. All rights reserved cally important pathogens of various crops. All definitive plant-infecting 0066-4170/09/0107-0447$20.00 and many vertebrate-infecting rhabdoviruses are persistently transmit- Annu. Rev. Entomol. 2009.54:447-468.
    [Show full text]
  • A Molecular Understanding of Alphavirus Entry
    Washington University School of Medicine Digital Commons@Becker Open Access Publications 10-1-2020 A molecular understanding of alphavirus entry Autumn C. Holmes Katherine Basore Daved H. Fremont Michael S. Diamond Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs PLOS PATHOGENS REVIEW A molecular understanding of alphavirus entry 1 2 2,3,4,5 Autumn C. HolmesID , Katherine Basore , Daved H. Fremont , Michael 1,2,3,5 S. DiamondID * 1 Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America, 2 Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America, 3 Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America, 4 Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States of America, 5 The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, Missouri, United States of America a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract a1111111111 Alphaviruses cause severe human illnesses including persistent arthritis and fatal encepha- litis. As alphavirus entry into target cells is the first step in infection, intensive research efforts have focused on elucidating aspects of this pathway, including attachment, internalization, OPEN ACCESS and fusion. Herein, we review recent developments in the molecular understanding of alpha- virus entry both in vitro and in vivo and how these advances might enable the design of ther- Citation: Holmes AC, Basore K, Fremont DH, Diamond MS (2020) A molecular understanding of apeutics targeting this critical step in the alphavirus life cycle.
    [Show full text]
  • Risk Groups: Viruses (C) 1988, American Biological Safety Association
    Rev.: 1.0 Risk Groups: Viruses (c) 1988, American Biological Safety Association BL RG RG RG RG RG LCDC-96 Belgium-97 ID Name Viral group Comments BMBL-93 CDC NIH rDNA-97 EU-96 Australia-95 HP AP (Canada) Annex VIII Flaviviridae/ Flavivirus (Grp 2 Absettarov, TBE 4 4 4 implied 3 3 4 + B Arbovirus) Acute haemorrhagic taxonomy 2, Enterovirus 3 conjunctivitis virus Picornaviridae 2 + different 70 (AHC) Adenovirus 4 Adenoviridae 2 2 (incl animal) 2 2 + (human,all types) 5 Aino X-Arboviruses 6 Akabane X-Arboviruses 7 Alastrim Poxviridae Restricted 4 4, Foot-and- 8 Aphthovirus Picornaviridae 2 mouth disease + viruses 9 Araguari X-Arboviruses (feces of children 10 Astroviridae Astroviridae 2 2 + + and lambs) Avian leukosis virus 11 Viral vector/Animal retrovirus 1 3 (wild strain) + (ALV) 3, (Rous 12 Avian sarcoma virus Viral vector/Animal retrovirus 1 sarcoma virus, + RSV wild strain) 13 Baculovirus Viral vector/Animal virus 1 + Togaviridae/ Alphavirus (Grp 14 Barmah Forest 2 A Arbovirus) 15 Batama X-Arboviruses 16 Batken X-Arboviruses Togaviridae/ Alphavirus (Grp 17 Bebaru virus 2 2 2 2 + A Arbovirus) 18 Bhanja X-Arboviruses 19 Bimbo X-Arboviruses Blood-borne hepatitis 20 viruses not yet Unclassified viruses 2 implied 2 implied 3 (**)D 3 + identified 21 Bluetongue X-Arboviruses 22 Bobaya X-Arboviruses 23 Bobia X-Arboviruses Bovine 24 immunodeficiency Viral vector/Animal retrovirus 3 (wild strain) + virus (BIV) 3, Bovine Bovine leukemia 25 Viral vector/Animal retrovirus 1 lymphosarcoma + virus (BLV) virus wild strain Bovine papilloma Papovavirus/
    [Show full text]
  • UC Berkeley UC Berkeley Electronic Theses and Dissertations
    UC Berkeley UC Berkeley Electronic Theses and Dissertations Title Mechanistic insights into the roles of P-TEFb and its novel cofactors in tumorigenesis and HIV transcription Permalink https://escholarship.org/uc/item/54n5v31q Author He, Nanhai Publication Date 2012 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California Mechanistic insights into the roles of P-TEFb and its novel cofactors in tumorigenesis and HIV transcription By Nanhai He A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Molecular and Cell Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Qiang Zhou, Chair Professor Mike Botchan Professor Tom Abler Professor Fenyong Liu Spring 2012 1 Abstract Mechanistic insights into the roles of P-TEFb and its novel cofactors in tumorigenesis and HIV transcription by Nanhai He Doctor of Philosophy in Molecular and Cell Biology University of California, Berkeley Professor Qiang Zhou, Chair Ongoing research in the field of transcription has given rise to the unappreciated role of elongation control as a rate limiting step for transcription, and the general transcription elongation factor P-TEFb therefore has taken the central stages. P-TEFb is composed of cyclin T1 and the cyclin-dependent kinase Cdk9. It stimulates transcription elongation by releasing the paused RNA Polymerase II (Pol II) through phosphorylating Pol II at Ser2 and antagonizing the effects of negative elongation factors. P-TEFb is not only essential for the transcription of the vast majority of cellular genes, but also critical for the expression of HIV genome.
    [Show full text]
  • Assessment of Vector Competence of UK Mosquitoes for Usutu Virus of African Origin Luis M
    Hernández-Triana et al. Parasites & Vectors (2018) 11:381 https://doi.org/10.1186/s13071-018-2959-5 SHORTREPORT Open Access Assessment of vector competence of UK mosquitoes for Usutu virus of African origin Luis M. Hernández-Triana1*, Maria Fernández de Marco1, Karen L. Mansfield1, Leigh Thorne1, Sarah Lumley1,2,3, Denise Marston1, Anthony A. Fooks1,4 and Nick Johnson1,2 Abstract Background: Usutu virus (USUV) is an emerging zoonotic virus originally from sub-Saharan Africa. It has been introduced into Europe on multiple occasions, causing substantial mortality within the Eurasian blackbird (Turdus merula) population. It is transmitted by the mosquito species Culex pipiens in Europe and Africa. Vector competence studies indicate that European strains of USUV are readily transmitted by indigenous Cx. pipiens. However, there is limited information on the ability of an African strain to infect European mosquitoes. Methods: We evaluated the ability of African strain SAAR-1776 to infect two lines of Cx. pipiens colonised within the United Kingdom (UK). Mosquitoes were fed blood meals containing this virus and maintained at 25 °C for up to 21 days. Individual mosquitoes were tested for the presence of virus in the body, legs and an expectorate saliva sample. Changes to the consensus of the virus genome were monitored in samples derived from infected mosquitoes using amplicon based next generation sequencing. Results: Infection, dissemination and the presence of virus in saliva in one mosquito line was observed, but no evidence for dissemination in the second mosquito line. This suggests a strong barrier to infection in UK Cx. pipiens for this strain of USUV.
    [Show full text]
  • UC Santa Cruz UC Santa Cruz Electronic Theses and Dissertations
    UC Santa Cruz UC Santa Cruz Electronic Theses and Dissertations Title Structural Studies Of Tetrahymena Thermophila Telomerase Permalink https://escholarship.org/uc/item/06s5j7vf Author Loper, John Anderson Publication Date 2013 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA SANTA CRUZ STRUCTURAL STUDIES OF TETRAHYMENA THERMOPHILA TELOMERASE A thesis submitted in partial satisfaction of the requirements for the degree of MASTER OF SCIENCE in CHEMISTRY by John A. Loper June 2013 The Thesis of John A. Loper is approved: Assistant Professor Michael D. Stone, Chair Professor Harry F. Noller Associate Professor Seth M. Rubin Tyrus Miller Vice Provost and Dean of Graduate Studies Table of Contents Chapter 1. Introduction …………...……………………………………………..... 1 1.0 Telomeres ……………………………………………………………….. 2 1.1 Telomerase ………………………………………....…………………… 3 1.1.1 Telomerase RNA (TER) ……………………………...……… 4 1.1.2 Telomerase Reverse Transcriptase (TERT) ……...………… 5 1.2 Telomerase and Human Disease ………………………………….....… 6 1.3 Tetrahymena thermophila Telomerase ………………………................ 7 1.4 References ………………………………………….......................…… 11 Chapter 2. The C-terminal Domain of p65 is Required and Sufficient for TER Rearrangement and TERT Recruitment …………………………………....… 16 2.0 Introduction …………………………………………………..……… 17 2.0.1 p65 …………………………………...................…………… 17 2.0.2 FRET ………………………………................……………… 18 2.1 Results ………………………………………………………………… 20 iii 2.1.1 Role
    [Show full text]
  • The Yeast La Related Protein Slf1p Is a Key Activator of Translation During the Oxidative Stress Response
    The Yeast La Related Protein Slf1p Is a Key Activator of Translation during the Oxidative Stress Response Christopher J. Kershaw1, Joseph L. Costello1¤, Lydia M. Castelli1, David Talavera1, William Rowe1, Paul F. G. Sims2, Mark P. Ashe1, Simon J. Hubbard1, Graham D. Pavitt1, Chris M. Grant1* 1 Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom, 2 Faculty of Life Sciences, Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, United Kingdom Abstract The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Slf1p and Sro9p are atypical-La motif containing proteins which are members of a superfamily of RNA-binding proteins conserved in eukaryotes. RIP-Seq analysis of these two yeast proteins identified overlapping and distinct sets of mRNA targets, including highly translated mRNAs such as those encoding ribosomal proteins. In paralell, transcriptome analysis of slf1D and sro9D mutant strains indicated altered gene expression in similar functional classes of mRNAs following loss of each factor. The loss of SLF1 had a greater impact on the transcriptome, and in particular, revealed changes in genes involved in the oxidative stress response. slf1D cells are more sensitive to oxidants and RIP-Seq analysis of oxidatively stressed cells enriched Slf1p targets encoding antioxidants and other proteins required for oxidant tolerance. To quantify these effects at the protein level, we used label-free mass spectrometry to compare the proteomes of wild-type and slf1D strains following oxidative stress. This analysis identified several proteins which are normally induced in response to hydrogen peroxide, but where this increase is attenuated in the slf1D mutant.
    [Show full text]