Phosphorylation of the Budgerigar Fledgling Disease Virus Major Capsid Protein Vp1t

Total Page:16

File Type:pdf, Size:1020Kb

Phosphorylation of the Budgerigar Fledgling Disease Virus Major Capsid Protein Vp1t JOURNAL OF VIROLOGY, JUIY 1992, p. 4551-4555 Vol. 66, No. 7 0022-538X/92/074551-05$02.00/0 Copyright © 1992, American Society for Microbiology Phosphorylation of the Budgerigar Fledgling Disease Virus Major Capsid Protein VP1t JOHN I. HAYNES II AND RICHARD A. CONSIGLI* Division of Biology, Section of Virology and Oncology, Ackert Hall, Kansas State University, Manhattan, Kansas 66506-4901 Received 19 February 1992/Accepted 30 March 1992 The structural proteins of the budgerigar fledgling disease virus, the first known nonmammalian polyoma- virus, were analyzed by isoelectric focusing and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The major capsid protein VP1 was found to be composed of at least five distinct species having isoelectric points ranging from pH 6.45 to 5.85. By analogy with the murine polyomavirus, these species apparently result from different modifications of an initial translation product. Primary chicken embryo cells were infected in the presence of 32p; to determine whether the virus structural proteins were modified by phosphorylation. SDS-PAGE of the purified virus structural proteins demonstrated that VP1 (along with both minor capsid proteins) was phosphorylated. Two-dimensional analysis of the radiolabeled virus showed phosphorylation of only the two most acidic isoelectric species of VP1, indicating that this posttranslational modification contributes to VP1 species heterogeneity. Phosphoamino acid analysis of 32P-labeled VP1 revealed that phosphoserine is the only phosphoamino acid present in the VP1 protein. Budgerigar fledgling disease virus (BFDV) has been iso- murine counterpart revealed 47% identity between the VP1 lated from fledgling budgerigars (Melopsittacus undulatus) proteins and 26.5 and 29.5% identity between the VP2 and showing lesions in numerous tissues, including skin, feather, VP3 proteins, respectively (35). follicle, kidney, uropygial gland, crop, liver, heart, bone Previous studies (1, 2, 4, 15, 24-26, 32, 41) have demon- marrow, spleen, and brain (3, 9, 10, 17, 33). BFDV, the first strated that the major capsid protein of the mouse polyoma- reported nonmammalian polyomavirus, can cause mortality virus is differentially modified after translation in several rates of up to 100% in budgerigar aviaries (3, 5, 9, 10, 18, 33). ways, including phosphorylation (1, 2, 4, 15, 24, 32). These Its classification as a polyomavirus is based on electron modifications are believed to contribute to the existence of at microscopic studies of its morphology, its resistance to least six species of the protein, which can be separated by organic solvents, its ability to replicate in the nuclei of isoelectric focusing (4). In the murine polyomavirus, these infected cells, the buoyant density of virions (1.34 g/ml), and species have been designated A (most basic) to F (most the characteristics of its DNA, which is supercoiled, with a acidic). Two-dimensional analysis of SV40 VP1 also re- molecular weight of 330,000 (5, 11, 22). In addition, Lehn vealed the presence of several different isoelectric forms of and Muller (22) were able to demonstrate transformation of this protein (31). SV40 VP1, like polyomavirus VP1, was nonpermissive primary hamster embryo fibroblasts by shown to be differentially phosphorylated (32). It was thus of BFDV. interest to determine whether VP1 of the avian polyomavirus Elucidation of the complete nucleotide sequence (35) of BFDV also undergoes modification by phosphorylation. We BFDV revealed similarities with both simian virus 40 (SV40) also wished to investigate the possible existence of multiple and murine polyomavirus. The DNA contains 4,980 bp and, isoelectric species of BFDV VP1 which may be differentially like those of the related viruses, is divided into early and late phosphorylated. coding regions. The early region codes for two proteins, For purification of BFDV, primary cultures of chicken which have been designated the large T and small T antigens embryo cells were prepared as described previously (29). by analogy with other papovaviruses. However, the large T Infected cultures were maintained at 39°C in serum-free antigen of BFDV is considerably smaller than the large T Dulbecco's modified Eagle's medium (DMEM). BFDV was antigen of either SV40 or polyomavirus. Another distinction purified from infected-cell lysates as described previously is that an open reading frame for middle T antigen found in for polyomavirus (28). The CsCl gradients used in the rodent polyomaviruses is not present in the BFDV genome. purification were prepared by the method of Brunck and The late region of the genome codes for three structural Leick (7) as described in greater detail elsewhere (6). Prior to proteins, VP1, VP2, and VP3, with apparent molecular CsCl purification, sucrose-pelleted virus was treated with a masses of 42, 39, and 29 kDa, respectively. As with SV40 1:1 mixture of phosphate-buffered saline (PBS; 10 mM and mouse polyomavirus, VP3 appears to be identical to the sodium phosphate [pH 7.2], 150 mM NaCl) and RIPA buffer carboxy terminus of VP2. Recently, a sequence in the (20 mM morpholinepropanesulfonic acid [MOPS, pH 7.0], carboxy terminus of VP2 has been shown to confer nuclear 150 mM NaCl, 1% [wt/vol] desoxycholate, 1% [vol/vol] localization on this protein (34). A comparison of the struc- Nonidet P-40, 0.1% sodium dodecyl sulfate [SDS], 2 mM tural proteins between this avian polyomavirus and its EDTA) containing 10 ,ug each of the protease inhibitors aprotinin, N-tosyl-L-lysine chloromethyl ketone, N-tosyl-L- phenylalanine chloromethyl ketone, and phenylmethylsulfo- * Corresponding author. nyl fluoride per ml. The lower band, containing intact BFDV t Contribution 92-439-J from the Kansas Agricultural Experiment virions, was collected from the CsCl gradients and used for Station, Kansas State University, Manhattan, KS 66506. all subsequent analyses. 4551 4552 NOTES J. VIROL. A. TABLE 1. Characteristics of BFDV virion VP1 isoelectric species Species Apparent pla 3P incorporated' 66- B. A 6.45 B 6.30 :-;: A B C D E vvv C 6.15 45I -VP,, - D 6.05 + E 5.85 + 245- 29- 4444! -VP3 a Apparent pls were determined by incubating a gel slice containing the respective species in 1 ml of distilled water and measuring the pH at room temperature. b Determined by autoradiography of in vivo 32P-labeled BFDV virions 214- electrophoresed on an O'Farrell (30) two-dimensional gel. -, nonphosphory- lated species; +, phosphorylated species. FIG. 1. Electrophoretic analysis of BFDV structural proteins. (A) The three BFDV structural proteins and host-contributed his- was then measured in distilled water. The pIs of the five tones were resolved by SDS-PAGE (12.5% polyacrylamide) (21) and isoelectric species of VP1 ranged from 6.45 to 5.85, as shown visualized by Coomassie blue staining. Sizes (in kilodaltons) were 1. The minor were also shown to obtained Dalton Mark VII-L molecular size' in Table capsid proteins by electrophoresing within this range shown in so estima- markers (Sigma) in an adjacent lane, and the BFDV structural have pIs (as Fig. 2B), proteins and host-contributed histones are indicated. (B) The five tion of their pIs was made by comparing their positions in the isoelectric species of BFDV VP1 (designated A [most basic] to E IEF dimension with the positions of the VP1 species. [most acidic]) were resolved by IEF in the first dimension and To study protein phosphorylation, BFDV was labeled in SDS-PAGE in the second dimension and visualized by Coomassie vivo with 3 Pi by removing the serum-free DMEM from blue staining. chicken embryo cells at 18 h postinfection and replacing the medium with serum-free Eagle's medium containing 20% of the normal phosphate concentration and supplemented with SDS-polyacrylamide gel electrophoresis (SDS-PAGE) (21) approximately 3.6 x 108 cpm of 32p; (carrier free; ICN was performed on purified BFDV virions with a 12.5% Radiochemicals, Irvine, Calif.) per 100-mm2 dish. Infection acrylamide gel and a 0.33% bisacrylamide cross-linker. The was allowed to proceed until the cultures showed cytopathic three BFDV structural proteins as well as the host-contrib- effect, at which time the cells were harvested and the virus uted histones are shown in Fig. 1A. The VPlIVP2NVP3 ratio was purified as described above. appears to be quite similar to that found in the murine For analysis of phosphorylation by SDS-PAGE, 2.5 x 104 polyomavirus and SV40 (40), with the maj'or capsid protein cpm of purified intact 32P-labeled virions was first immuno- VP1 constituting at least 75% of the total protein of all three precipitated with anti-BFDV VP1 monoclonal antibody viruses. In order to determine whether isoelectric heteroge- 4F10F4 (13) to eliminate possible contaminating cellular neity exists in the BFDV major capsid protein, as it does in proteins. Four volumes of RIPA buffer were added to the murine polyomavirus and SV40, two-dimensional electro- mixture, which was then rocked at 4°C for 2 h, after which 50 phoresis wa's performed on purified virus by the method of pl of a 20% suspension of Staphylococcus aureus Pansorbin O'Farrell,, essentially as described previously (2, 4, 12, 30). cells (Calbiochem, San Diego, Calif.) in RIPA buffer was Prior to electrophoresis, 20 p.g of BFDV virions was dis- added. The mixture was rocked at 4°C for an additional 45 rupted in 2% SDS-5% 2-mercaptoethanol for 2 min at 1000C min, and the particulate material was pelleted by centrifuga- and acetone precipitated. The viral pellets were then resus- tion and washed three times in RIPA buffer, twice in PBS, pended in a 25-pAl solution composed of 9.5 M urea, 5% and once in distilled water. The final pellet was resuspended 2-mercaptoethanol, 2% Nonidet P-40, and 2% ampholines. in SDS-PAGE sample buffer (21), boiled for 2 min to elute The ampholine mixture used for isoelectric focusing (IEF) the antigen-antibody complexes from the cells, and recentri- consisted of equal volumes of pH 2.5-5 (Pharmacia), pH 4-6 fuged.
Recommended publications
  • The Polyomavirus Major Capsid Protein VP1 Interacts with the Nuclear Matrix Regulatory Protein
    FEBS 23316 FEBS Letters 467 (2000) 359^364 View metadata, citation and similar papers at core.ac.uk brought to you by CORE The polyomavirus major capsid protein VP1 interacts with theprovided nuclearby Elsevier - Publisher Connector matrix regulatory protein YY1 Zdena Palkova¨a;b, Hana Sípanielova¨b, Vanesa Gottifredia;1, Dana Hollanderova¨b, Jitka Forstova¨b, Paolo Amatia;* aInstituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Universita© di Roma La Sapienza, Viale Regina Elena 324, 00161 Rome, Italy bDepartment of Genetics and Microbiology, Faculty of Natural Sciences, Charles University, Vinie©na¨ 5, 12844 Prague 2, Czech Republic Received 17 December 1999 Edited by Hans-Dieter Klenk The external loops are likely to be the structures involved in Abstract Polyomavirus reaches the nucleus in a still encapsi- dated form, and the viral genome is readily found in association cell receptor recognition by virions [4] and, therefore, to be with the nuclear matrix. This association is thought to be the main antigenic determinants. The £exible C-terminal arms essential for viral replication. In order to identify the protein(s) form interpentameric contacts and the basic amino acids of involved in the virus-nuclear matrix interaction, we focused on the N terminal arm are responsible for the non-speci¢c DNA- the possible roles exerted by the multifunctional cellular nuclear binding activity of VP1 [6,7]. matrix protein Yin Yang 1 (YY1) and by the viral major capsid The necessity for viral genomes to associate to the nuclear protein VP1. In the present work we report on the in vivo matrix (NM) in order to be expressed, has been demonstrated association between YY1 and VP1.
    [Show full text]
  • Cryptic Inoviruses Revealed As Pervasive in Bacteria and Archaea Across Earth’S Biomes
    ARTICLES https://doi.org/10.1038/s41564-019-0510-x Corrected: Author Correction Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes Simon Roux 1*, Mart Krupovic 2, Rebecca A. Daly3, Adair L. Borges4, Stephen Nayfach1, Frederik Schulz 1, Allison Sharrar5, Paula B. Matheus Carnevali 5, Jan-Fang Cheng1, Natalia N. Ivanova 1, Joseph Bondy-Denomy4,6, Kelly C. Wrighton3, Tanja Woyke 1, Axel Visel 1, Nikos C. Kyrpides1 and Emiley A. Eloe-Fadrosh 1* Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach lever- aging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem.
    [Show full text]
  • Opportunistic Intruders: How Viruses Orchestrate ER Functions to Infect Cells
    REVIEWS Opportunistic intruders: how viruses orchestrate ER functions to infect cells Madhu Sudhan Ravindran*, Parikshit Bagchi*, Corey Nathaniel Cunningham and Billy Tsai Abstract | Viruses subvert the functions of their host cells to replicate and form new viral progeny. The endoplasmic reticulum (ER) has been identified as a central organelle that governs the intracellular interplay between viruses and hosts. In this Review, we analyse how viruses from vastly different families converge on this unique intracellular organelle during infection, co‑opting some of the endogenous functions of the ER to promote distinct steps of the viral life cycle from entry and replication to assembly and egress. The ER can act as the common denominator during infection for diverse virus families, thereby providing a shared principle that underlies the apparent complexity of relationships between viruses and host cells. As a plethora of information illuminating the molecular and cellular basis of virus–ER interactions has become available, these insights may lead to the development of crucial therapeutic agents. Morphogenesis Viruses have evolved sophisticated strategies to establish The ER is a membranous system consisting of the The process by which a virus infection. Some viruses bind to cellular receptors and outer nuclear envelope that is contiguous with an intri‑ particle changes its shape and initiate entry, whereas others hijack cellular factors that cate network of tubules and sheets1, which are shaped by structure. disassemble the virus particle to facilitate entry. After resident factors in the ER2–4. The morphology of the ER SEC61 translocation delivering the viral genetic material into the host cell and is highly dynamic and experiences constant structural channel the translation of the viral genes, the resulting proteins rearrangements, enabling the ER to carry out a myriad An endoplasmic reticulum either become part of a new virus particle (or particles) of functions5.
    [Show full text]
  • Receptor-Binding and Oncogenic Properties of Polyoma Viruses Isolated from Feral Mice
    Receptor-Binding and Oncogenic Properties of Polyoma Viruses Isolated from Feral Mice John Carroll1[, Dilip Dey1[, Lori Kreisman1[, Palanivel Velupillai1, Jean Dahl1, Samuel Telford2, Roderick Bronson1, Thomas Benjamin1* 1 Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America, 2 Department of Tropical Public Health, Harvard School of Public Health, Boston, Massachusetts, United States of America Laboratory strains of the mouse polyoma virus differ markedly in their abilities to replicate and induce tumors in newborn mice. Major determinants of pathogenicity lie in the sialic binding pocket of the major capsid protein Vp1 and dictate receptor-binding properties of the virus. Substitutions at two sites in Vp1 define three prototype strains, which vary greatly in pathogenicity. These strains replicate in a limited fashion and induce few or no tumors, cause a disseminated infection leading to the development of multiple solid tumors, or replicate and spread acutely causing early death. This investigation was undertaken to determine the Vp1 type(s) of new virus isolates from naturally infected mice. Compared with laboratory strains, truly wild-type viruses are constrained with respect to their selectivity and avidity of binding to cell receptors. Fifteen of 15 new isolates carried the Vp1 type identical to that of highly tumorigenic laboratory strains. Upon injection into newborn laboratory mice, the new isolates induced a broad spectrum of tumors, including ones of epithelial as well as mesenchymal origin. Though invariant in their Vp1 coding sequences, these isolates showed considerable variation in their regulatory sequences. The common Vp1 type has two essential features: 1) failure to recognize ‘‘pseudoreceptors’’ with branched chain sialic acids binding to which would attenuate virus spread, and 2) maintenance of a hydrophobic contact with true receptors bearing a single sialic acid, which retards virus spread and avoids acute and potentially lethal infection of the host.
    [Show full text]
  • REVIEW Hepatitis C Virus
    DOI:http://dx.doi.org/10.7314/APJCP.2012.13.12.5917 Hepatitis C Virus -Proteins, Diagnosis, Treatment and New Approaches for Vaccine Development REVIEW Hepatitis C Virus - Proteins, Diagnosis, Treatment and New Approaches for Vaccine Development Hossein Keyvani1, Mehdi Fazlalipour2*, Seyed Hamid Reza Monavari1, Hamid Reza Mollaie2 Abstract Background: Hepatitis C virus (HCV) causes acute and chronic human hepatitis infection and as such is an important global health problem. The virus was discovered in the USA in 1989 and it is now known that three to four million people are infected every year, WHO estimating that 3 percent of the 7 billion people worldwide being chronically infected. Humans are the natural hosts of HCV and this virus can eventually lead to permanent liver damage and carcinoma. HCV is a member of the Flaviviridae family and Hepacivirus genus. The diameter of the virus is about 50-60 nm and the virion contains a single-stranded positive RNA approximately 10,000 nucleotides in length and consisting of one ORF which is encapsulated by an external lipid envelope and icosahedral capsid. HCV is a heterogeneous virus, classified into 6 genotypes and more than 50 subtypes. Because of the genome variability, nucleotide sequences of genotypes differ by approximately 31-34%, and by 20-23% among subtypes. Quasi-species of mixed virus populations provide a survival advantage for the virus to create multiple variant genomes and a high rate of generation of variants to allow rapid selection of mutants for new environmental conditions. Direct contact with infected blood and blood products, sexual relationships and availability of injectable drugs have had remarkable effects on HCV epidemiology.
    [Show full text]
  • Structural Basis and Evolution of Glycan Receptor Specificities Within the Polyomavirus Family
    RESEARCH ARTICLE Host-Microbe Biology crossm Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family Luisa J. Ströh,a* Nils H. Rustmeier,a Bärbel S. Blaum,a Josephine Botsch,a Philip Rößler,a Florian Wedekink,a W. Ian Lipkin,b Nischay Mishra,b Thilo Stehlea,c Downloaded from aInterfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany bCenter for Infection and Immunity, Columbia University, New York, New York, USA cDepartment of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA ABSTRACT Asymptomatic infections with polyomaviruses in humans are common, but these small viruses can cause severe diseases in immunocompromised hosts. New Jersey polyomavirus (NJPyV) was identified via a muscle biopsy in an organ transplant recipient with systemic vasculitis, myositis, and retinal blindness, and hu- http://mbio.asm.org/ man polyomavirus 12 (HPyV12) was detected in human liver tissue. The evolutionary origins and potential diseases are not well understood for either virus. In order to define their receptor engagement strategies, we first used nuclear magnetic reso- nance (NMR) spectroscopy to establish that the major capsid proteins (VP1) of both viruses bind to sialic acid in solution. We then solved crystal structures of NJPyV and HPyV12 VP1 alone and in complex with sialylated glycans. NJPyV employs a novel binding site for a ␣2,3-linked sialic acid, whereas HPyV12 engages terminal ␣2,3- or ␣2,6-linked sialic acids in an exposed site similar to that found in Trichodysplasia on October 12, 2020 by guest spinulosa-associated polyomavirus (TSPyV). Gangliosides or glycoproteins, featuring in mammals usually terminal sialic acids, are therefore receptor candidates for both viruses.
    [Show full text]
  • Protein-Mediated Viral Latency Is a Novel Mechanism for Merkel Cell
    Protein-mediated viral latency is a novel mechanism PNAS PLUS for Merkel cell polyomavirus persistence Hyun Jin Kwuna, Yuan Changa,1,2, and Patrick S. Moorea,1,2 aCancer Virology Program, University of Pittsburgh, Pittsburgh, PA 15213 Contributed by Patrick S. Moore, April 10, 2017 (sent for review March 8, 2017; reviewed by Daniel DiMaio and Peter M. Howley) Viral latency, in which a virus genome does not replicate in- binding. Expression of LT is known to be autoinhibited in two ways: dependently of the host cell genome and produces no infectious LT inhibits its own promoter in a negative feedback loop (5, 6), and particles, is required for long-term virus persistence. There is no a virus-encoded miRNA transcribed during early viral gene ex- known latency mechanism for chronic small DNA virus infections. pression inhibits LT mRNA expression (7–10). Merkel cell polyomavirus (MCV) causes an aggressive skin cancer Merkel cell polyomavirus (MCV) is a human polyomavirus that after prolonged infection and requires an active large T (LT) phos- causes ∼80% of human Merkel cell carcinomas (MCCs), which phoprotein helicase to replicate. We show that evolutionarily are among the most severe skin cancers (11, 12). It was the first conserved MCV LT phosphorylation sites are constitutively recog- human pathogen discovered through nondirected transcriptome nized by cellular Fbw7, βTrCP, and Skp2 Skp-F-box-cullin (SCF) sequencing using an approach called digital transcriptome sub- E3 ubiquitin ligases, which degrade and suppress steady-state LT traction. MCV infection is nearly ubiquitous among human adults, protein levels. Knockdown of each of these E3 ligases enhances LT and MCC tumors arise as rare biological accidents after prolonged stability and promotes MCV genome replication.
    [Show full text]
  • High Aspect Ratio Viral Nanoparticles for Cancer Therapy
    HIGH ASPECT RATIO VIRAL NANOPARTICLES FOR CANCER THERAPY By Karin L. Lee Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Dissertation Advisor: Dr. Nicole F. Steinmetz Biomedical Engineering CASE WESTERN RESERVE UNIVERSITY August 2016 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of Karin L. Lee candidate for the Doctor of Philosophy degree*. (signed) Horst von Recum (chair of the committee) Nicole Steinmetz Ruth Keri David Schiraldi (date) June 29, 2016 *We also certify that written approval has been obtained for any proprietary material contained therein. TABLE OF CONTENTS Table of Contents List of Tables .................................................................................................................... ix List of Figures and Schemes .............................................................................................x Acknowledgements ........................................................................................................ xiv List of Abbreviations .................................................................................................... xvii Abstract......................................................................................................................... xxiii Chapter 1: Introduction ....................................................................................................1 1.1 Cancer statistics...............................................................................................................1
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 7,527,801 B2 Coit Et Al
    USOO7527801B2 (12) United States Patent (10) Patent No.: US 7,527,801 B2 Coit et al. (45) Date of Patent: May 5, 2009 (54) NOROVIRUS AND SAPOVIRUS ANTIGENS Genbank Accession # AAQ63158, ORF3 of Norwalk virus, pub lished Aug. 31, 2003.* (75) Inventors: Doris Coit, Petaluma, CA (US); Glass et al., Two Nonoverlapping Domains on the Norwalk Virus Michael Houghton, Danville, CA (US); Open Reading Frame 3 (ORF3) Protein Are Involved in the Forma Colin McCoin, Castro Valley, CA (US); tion of the Phosphorylated 35K Protein and in ORF3-Capsid Protein Interactions, 2003, Journal of Virology, vol. 77. No. 6, pp. 3569 Angelica Medina-Selby, San Francisco, 3577.: CA (US); Michael Vajdy, Orinda, CA Harrington et al., Systemic, Mucosal, and Heterotypic Immune (US) Induction in Mice Inoculated with Venezuelan Equine Encephalitis Replicons ExpressingNorwalkVirus-Like Particles, 2002, Journal of (73) Assignee: Novartis Vaccines and Diagnostics, Virology, vol. 76, No. 2, pp. 730-742.* Inc., Emeryville, CA (US) Asanaka, et al., “Replication And Packaging Of Norwalk Virus RNA In Cultured Mammalian Cells. PNAS USA 102: 10327-10332 (*) Notice: Subject to any disclaimer, the term of this (2005). patent is extended or adjusted under 35 Belliot, et al., “In Vitro Proteolytic Processing Of The MD 145 U.S.C. 154(b) by 0 days. Norovirus ORF1 Nonstructural Polyprotein Yields Stable Precursors And Products Similar To Those Detected In Calicivirus-Infected (21) Appl. No.: 11/603.913 Cells.”J Virol 77: 10957-10974 (2003). Chakravarty, et al., “Evolutionary Trace Residues. In Noroviruses: (22) Filed: Nov. 22, 2006 Importance In Receptor Binding, Antigenicity, Virion Assembly, And Strain Diversity.”J Virol 79:554-568 (2005).
    [Show full text]
  • Nucleotide Substitution Rates of HIV-1
    AIDS Rev 2000; 2: 39-47 Nucleotide Substitution Rates of HIV-1 Yoshiyuki Suzuki1, Yumi Yamaguchi-Kabata2, and Takashi Gojobori1 1Center for Information Biology, National Institute of Genetics, Mishima, Japan 2Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, Japan Abstract The molecular evolution of human immunodeficiency virus type 1 (HIV-1) is reviewed from the viewpoint of the rate of nucleotide substitution, which is defined as the number of nucleotide substitutions per site per year. The rate of nucleotide substitution is useful not only for estimating the origin and history of HIV-1 epidemics, but also for detecting natural selection operating at the amino acid sequence level. The RNA viruses may be classified into two groups, the rapidly and slowly evolving RNA viruses, according to their rates of nucleotide substitution; 10-3-10-4 and 10-6-10-7 per site per year for the former and the latter, respectively. HIV-1 is a member of the rapidly evolving RNA viruses, with the rate of 10-3 per site per year, which is several million times faster than the eukaryotic and prokaryotic genes. The linear regression analysis of a large number of HIV-1 sequences revealed that HIV-1 has a weak molecular clock. The latest divergence time between human immunodeficiency virus type 2 (HIV-2) and simian immunodeficiency virus (SIV) was estimated as about 30 years ago, and that between HIV-1 and SIV as several hundred years ago. These observations, as well as the inconsistency between the topologies of phylogenetic trees reconstructed for primate lentiviruses and for their host species, indicate that the interspecies transmission occurred during the evolution of primate lentiviruses.
    [Show full text]
  • Structural Presentation of Influenza Epitopes on Modular Virus-Like Particles Doan Thanh Tam Master of Biotechnology
    Structural presentation of influenza epitopes on modular virus-like particles Doan Thanh Tam Master of Biotechnology A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2018 Australian Institute for Bioengineering and Nanotechnology i Abstract Vaccine development has increasingly developed toward subunit vaccine approach which uses highly-purified and well-characterised components, such as antigenic peptides, to elicit an immune response. An antigenic peptide requires a protein carrier or platform e.g. virus-like particle (VLP), to improve its poor immunogenicity. Based on this approach, murine polyomavirus (MuPyV) VLP and its subunit (capsomere) have been employed as vaccine platforms to present heterogeneous epitopes or antigenic elements from targeted pathogens. The design rule for epitope presentation on VLPs still remains unclear. A tandem repeat display strategy, in which antigenic element was repetitively arrayed, led to the induction of a significant antibody titer against its native structure, compared with the use of flanking sequence. Tandem repeat display strategy might retain the epitope conformation that is close to its native structure. This work further investigates the structural presentation of Helix 190 (H190) and Helix A (HA2A), from influenza hemagglutinin, using tandem repeat strategy. Different tools are exploited to characterise the structures of presented epitopes. The major outcomes of this research are: (i) demonstrating the limitation of phage antibody panning as a tool to inform the structural presentation of epitope on modular VLPs; (ii) developing a simple tool for rapid screening of presented epitope conformation using circular dichroism spectroscopy coupled with singular value decomposition algorithms (CD-SVD); (iii) demonstrating the capability of tandem repeat strategy in promoting the helicity of the helical structure; (iv) establishing initial steps in determining atomic structure of presented epitope using X-ray crystallography.
    [Show full text]
  • Resurrection of a Global, Metagenomically Defined Microvirus 1 2 3 4 Paul C. Kirchberger* and Howard Ochman 5 6 7 8 9 Department
    bioRxiv preprint doi: https://doi.org/10.1101/743518; this version posted August 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Resurrection of a Global, Metagenomically Defined Microvirus 2 3 4 5 Paul C. Kirchberger* and Howard Ochman 6 7 8 9 10 Department of Integrative Biology 11 University of Texas at Austin 12 Austin, Texas 78712, USA 13 14 15 16 17 18 *Corresponding author. Email: [email protected] 19 bioRxiv preprint doi: https://doi.org/10.1101/743518; this version posted August 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 20 Abstract 21 The Gokushovirinae (family Microviridae) are a group of single-stranded, circular 22 DNA bacteriophages that have been detected in metagenomic datasets from every 23 ecosystem on the planet. Despite their abundance, little is known about their biology or 24 their bacterial hosts: isolates are exceedingly rare, known only from a very small 25 number of obligate intracellular bacteria. By synthesizing circularized phage genomes 26 from prophages embedded in diverse enteric bacteria, we produced viable 27 gokushovirus phage particles that could reliably infect E. coli, thereby allowing 28 experimental analysis of its life cycle and growth characteristics.
    [Show full text]