A distinct class of internal ribosomal entry site in members of the Kobuvirus and proposed Salivirus and Paraturdivirus genera of the Picornaviridae.

Abstract:

:The 5'-untranslated regions (5' UTRs) of picornavirus genomes contain an internal ribosomal entry site (IRES) that promotes the end-independent initiation of translation. Picornavirus IRESs are classified into four structurally distinct groups, each with different initiation factor requirements. Here, we identify a fifth IRES class in members of Kobuvirus, Salivirus, and Paraturdivirus genera of Picornaviridae: Aichi virus (AV), bovine kobuvirus (BKV), canine kobuvirus (CKoV), mouse kobuvirus (MKoV), sheep kobuvirus (SKV), salivirus A (SV-A), turdivirus 2 (TV2), and TV3. The 410-nucleotide (nt)-long AV IRES comprises four domains (I to L), including a hairpin (L) that overlaps a Yn-Xm-AUG (pyrimidine tract/spacer/initiation codon) motif. SV-A, CKoV, and MKoV also contain these four domains, whereas BKV, SKV, and TV2/TV3 5' UTRs contain domains that are related to domain I and equivalent to domains J and K but lack an AV-like domain L. These IRESs are located at different relative positions between a conserved 5'-terminal origin of replication and divergent coding sequences. Elements in these IRESs also occur elsewhere: domain J's apical subdomain, which contains a GNRA tetraloop, matches an element in type 1 IRESs, and eIF4G-binding motifs in domain K and in type 2 IRESs are identical. Other elements are unique, and their presence leads to unique initiation factor requirements. In vitro reconstitution experiments showed that like AV, but in contrast to other currently characterized IRESs, SV-A requires the DExH-box protein DHX29 during initiation, which likely ensures that the initiation codon sequestered in domain L is properly accommodated in the ribosomal mRNA-binding cleft.

journal_name

J Virol

journal_title

Journal of virology

authors

Sweeney TR,Dhote V,Yu Y,Hellen CU

doi

10.1128/JVI.05862-11

subject

Has Abstract

pub_date

2012-02-01 00:00:00

pages

1468-86

issue

3

eissn

0022-538X

issn

1098-5514

pii

JVI.05862-11

journal_volume

86

pub_type

杂志文章
  • Role of CD8+ T cells and lymphoid dendritic cells in protection from ocular herpes simplex virus 1 challenge in immunized mice.

    abstract::The development of immunization strategies to protect against ocular infection with herpes simplex virus 1 (HSV-1) must address the issue of the effects of the strategy on the establishment of latency in the trigeminal ganglia (TG). It is the reactivation of this latent virus that can cause recurrent disease and corne...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.00913-14

    authors: Matundan H,Mott KR,Ghiasi H

    更新日期:2014-07-01 00:00:00

  • Characterization of the Herpes Simplex Virus (HSV) Tegument Proteins That Bind to gE/gI and US9, Which Promote Assembly of HSV and Transport into Neuronal Axons.

    abstract::The herpes simplex virus (HSV) heterodimer gE/gI and another membrane protein, US9, which has neuron-specific effects, promote the anterograde transport of virus particles in neuronal axons. Deletion of both HSV gE and US9 blocks the assembly of enveloped particles in the neuronal cytoplasm, which explains why HSV vir...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.01113-20

    authors: DuRaine G,Wisner TW,Johnson DC

    更新日期:2020-11-09 00:00:00

  • The Epstein-Barr virus immediate-early protein BZLF1 induces expression of E2F-1 and other proteins involved in cell cycle progression in primary keratinocytes and gastric carcinoma cells.

    abstract::The Epstein-Barr virus (EBV) immediate-early protein BZLF1 mediates the switch between the latent and lytic forms of EBV infection and has been previously shown to induce a G(1)/S block in cell cycle progression in some cell types. To examine the effect of BZLF1 on cellular gene expression, we performed microarray ana...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/jvi.76.24.12543-12552.2002

    authors: Mauser A,Holley-Guthrie E,Zanation A,Yarborough W,Kaufmann W,Klingelhutz A,Seaman WT,Kenney S

    更新日期:2002-12-01 00:00:00

  • Evaluation of the Immune Responses to and Cross-Protective Efficacy of Eurasian H7 Avian Influenza Viruses.

    abstract::Due to increasing concerns about human infection by various H7 influenza viruses, including recent H7N9 viruses, we evaluated the genetic relationships and cross-protective efficacies of three different Eurasian H7 avian influenza viruses. Phylogenic and molecular analyses revealed that recent Eurasian H7 viruses can ...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.02259-16

    authors: Kwon HI,Kim YI,Park SJ,Song MS,Kim EH,Kim SM,Si YJ,Lee IW,Song BM,Lee YJ,Yun SJ,Kim WJ,Choi YK

    更新日期:2017-05-12 00:00:00

  • Epochal evolution of GGII.4 norovirus capsid proteins from 1995 to 2006.

    abstract::Noroviruses are the causative agents of the majority of viral gastroenteritis outbreaks in humans. During the past 15 years, noroviruses of genotype GGII.4 have caused four epidemic seasons of viral gastroenteritis, during which four novel variants (termed epidemic variants) emerged and displaced the resident viruses....

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.00674-07

    authors: Siebenga JJ,Vennema H,Renckens B,de Bruin E,van der Veer B,Siezen RJ,Koopmans M

    更新日期:2007-09-01 00:00:00

  • Clade-specific differences between human immunodeficiency virus type 1 clades B and C: diversity and correlations in C3-V4 regions of gp120.

    abstract::Current knowledge of human immunodeficiency virus type 1 envelope (Env) glycoprotein structure and function is based on studies of clade B viruses. We present evidence of sequence and structural differences in viral glycoprotein gp120 between clades B and C. In clade C, the C3 region alpha2-helix exhibits high sequenc...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.01954-06

    authors: Gnanakaran S,Lang D,Daniels M,Bhattacharya T,Derdeyn CA,Korber B

    更新日期:2007-05-01 00:00:00

  • Nonspecific down-regulation of CD8+ T-cell responses in mice expressing human papillomavirus type 16 E7 oncoprotein from the keratin-14 promoter.

    abstract::The E7 oncoprotein of human papillomavirus 16 (HPV16) transforms basal and suprabasal cervical epithelial cells and is a tumor-specific antigen in cervical carcinoma, to which immunotherapeutic strategies aimed at cytotoxic T-lymphocyte (CTL) induction are currently directed. By quantifying major histocompatibility co...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.75.13.5985-5997.2001

    authors: Tindle RW,Herd K,Doan T,Bryson G,Leggatt GR,Lambert P,Frazer IH,Street M

    更新日期:2001-07-01 00:00:00

  • High-level expression and purification of secreted forms of herpes simplex virus type 1 glycoprotein gD synthesized by baculovirus-infected insect cells.

    abstract::Two forms of herpes simplex virus glycoprotein gD were recombined into Autographa californica nuclear polyhedrosis virus (baculovirus) and expressed in infected Spodoptera frugiperda (Sf9) cells. Each protein was truncated at residue 306 of mature gD. One form, gD-1(306t), contains the coding sequence of Patton strain...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.68.2.766-775.1994

    authors: Sisk WP,Bradley JD,Leipold RJ,Stoltzfus AM,Ponce de Leon M,Hilf M,Peng C,Cohen GH,Eisenberg RJ

    更新日期:1994-02-01 00:00:00

  • An internally located RNA hairpin enhances replication of Tomato bushy stunt virus RNAs.

    abstract::Defective interfering (DI) RNAs of Tomato bushy stunt virus (TBSV), a plus-sense RNA virus, comprise four conserved noncontiguous regions (I through IV) derived from the viral genome. Region III, a 70-nucleotide-long sequence corresponding to a genomic segment located 378 nucleotides upstream of the 3' terminus of the...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/jvi.77.1.245-257.2003

    authors: Ray D,White KA

    更新日期:2003-01-01 00:00:00

  • Persistent and transient replication of full-length hepatitis C virus genomes in cell culture.

    abstract::The recently developed subgenomic hepatitis C virus (HCV) replicons were limited by the fact that the sequence encoding the structural proteins was missing. Therefore, important information about a possible influence of these proteins on replication and pathogenesis and about the mechanism of virus formation could not...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/jvi.76.8.4008-4021.2002

    authors: Pietschmann T,Lohmann V,Kaul A,Krieger N,Rinck G,Rutter G,Strand D,Bartenschlager R

    更新日期:2002-04-01 00:00:00

  • Role of Kaposi's sarcoma-associated herpesvirus C-terminal LANA chromosome binding in episome persistence.

    abstract::Kaposi's sarcoma-associated herpesvirus (KSHV) LANA is an 1,162-amino-acid protein that tethers terminal repeat (TR) DNA to mitotic chromosomes to mediate episome persistence in dividing cells. C-terminal LANA self-associates to bind TR DNA. LANA contains independent N- and C-terminal chromosome binding regions. N-ter...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.02395-08

    authors: Kelley-Clarke B,De Leon-Vazquez E,Slain K,Barbera AJ,Kaye KM

    更新日期:2009-05-01 00:00:00

  • Neutralizing IgG at the portal of infection mediates protection against vaginal simian/human immunodeficiency virus challenge.

    abstract::Neutralizing antibodies may have critical importance in immunity against human immunodeficiency virus type 1 (HIV-1) infection. However, the amount of protective antibody needed at mucosal surfaces has not been fully established. Here, we evaluated systemic and mucosal pharmacokinetics (PK) and pharmacodynamics (PD) o...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.01361-13

    authors: Klein K,Veazey RS,Warrier R,Hraber P,Doyle-Meyers LA,Buffa V,Liao HX,Haynes BF,Shaw GM,Shattock RJ

    更新日期:2013-11-01 00:00:00

  • Vertical transmission of bovine spongiform encephalopathy prions evaluated in a transgenic mouse model.

    abstract::In this work we show evidence of mother-to-offspring transmission in a transgenic mouse line expressing bovine PrP (boTg) experimentally infected by intracerebral administration of bovine spongiform encephalopathy (BSE) prions. PrP(res) was detected in brains of newborns from infected mothers only when mating was allo...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.79.13.8665-8668.2005

    authors: Castilla J,Brun A,Díaz-San Segundo F,Salguero FJ,Gutiérrez-Adán A,Pintado B,Ramírez MA,del Riego L,Torres JM

    更新日期:2005-07-01 00:00:00

  • Ultrastructural studies of a visna-like syncytia-producing virus from cattle with lymphocytosis.

    abstract::A virus structurally similar to viruses associated with maedi, progressive pneumonia, and visna of sheep has been isolated from buffy coat cells of cattle with chronic lymphocytosis. Electron microscope studies revealed three variants of the virion: (i) an intracytoplasmic form 98 to 116 nm in diameter when occurring ...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.13.1.197-204.1974

    authors: Boothe AD,Van der Maaten AJ

    更新日期:1974-01-01 00:00:00

  • Pathobiology of Clade 2.3.4.4 H5Nx High-Pathogenicity Avian Influenza Virus Infections in Minor Gallinaceous Poultry Supports Early Backyard Flock Introductions in the Western United States in 2014-2015.

    abstract::In 2014 and 2015, the United States experienced an unprecedented outbreak of Eurasian clade 2.3.4.4 H5 highly pathogenic avian influenza (HPAI) virus. Initial cases affected mainly wild birds and mixed backyard poultry species, while later outbreaks affected mostly commercial chickens and turkeys. The pathogenesis, tr...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.00960-17

    authors: Bertran K,Lee DH,Pantin-Jackwood MJ,Spackman E,Balzli C,Suarez DL,Swayne DE

    更新日期:2017-10-13 00:00:00

  • Characterization of the pneumococcal bacteriophage HB-3 amidase: cloning and expression in Escherichia coli.

    abstract::HB-3, a temperate bacteriophage of Streptococcus pneumoniae, synthesizes its own murein hydrolase activity when multiplying on cultures of pneumococcus. The enzyme (HBL) was purified and biochemically characterized as an N-acetylmuramoyl-L-alanine amidase of 36,000 daltons, and a 2.1-kilobase DraI fragment containing ...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.64.1.137-142.1990

    authors: Romero A,Lopez R,Garcia P

    更新日期:1990-01-01 00:00:00

  • Herpes Simplex Virus 1 Replication, Ocular Disease, and Reactivations from Latency Are Restricted Unilaterally after Inoculation of Virus into the Lip.

    abstract::Ocular herpes simplex keratitis (HSK) is a consequence of viral reactivations from trigeminal ganglia (TG) and occurs almost exclusively in the same eye in humans. In our murine oro-ocular (OO) model, herpes simplex virus 1 (HSV-1) inoculation in one side of the lip propagates virus to infect the ipsilateral TG. Repli...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.01586-19

    authors: Poccardi N,Rousseau A,Haigh O,Takissian J,Naas T,Deback C,Trouillaud L,Issa M,Roubille S,Juillard F,Efstathiou S,Lomonte P,Labetoulle M

    更新日期:2019-11-26 00:00:00

  • DNA repair enzyme uracil DNA glycosylase is specifically incorporated into human immunodeficiency virus type 1 viral particles through a Vpr-independent mechanism.

    abstract::The Vpr protein, encoded by the human immunodeficiency virus type 1 (HIV-1) genome, is one of the nonstructural proteins packaged in large amounts into viral particles. We have previously reported that Vpr associates with the DNA repair enzyme uracil DNA glycosylase (UDG). In this study, we extended these observations...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.73.2.1682-1688.1999

    authors: Willetts KE,Rey F,Agostini I,Navarro JM,Baudat Y,Vigne R,Sire J

    更新日期:1999-02-01 00:00:00

  • Kaposi's Sarcoma-Associated Herpesvirus Viral Interferon Regulatory Factor 4 (vIRF4) Perturbs the G1-S Cell Cycle Progression via Deregulation of the cyclin D1 Gene.

    abstract::Kaposi's sarcoma-associated herpesvirus (KSHV) infection modulates the host cell cycle to create an environment optimal for its viral-DNA replication during the lytic life cycle. We report here that KSHV vIRF4 targets the β-catenin/CBP cofactor and blocks its occupancy on the cyclin D1 promoter, suppressing the G1-S c...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.01897-15

    authors: Lee HR,Mitra J,Lee S,Gao SJ,Oh TK,Kim MH,Ha T,Jung JU

    更新日期:2015-10-21 00:00:00

  • Effects of viral strain, transgene position, and target cell type on replication kinetics, genomic stability, and transgene expression of replication-competent murine leukemia virus-based vectors.

    abstract::The limited efficiency of in vivo gene transfer by replication-deficient retroviral vectors remains an obstacle to achieving effective gene therapy for solid tumors. One approach to circumvent this problem is the use of replication-competent retroviral vectors. However, the application of such vectors is at a comparat...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.02470-06

    authors: Paar M,Schwab S,Rosenfellner D,Salmons B,Günzburg WH,Renner M,Portsmouth D

    更新日期:2007-07-01 00:00:00

  • Unusual Features of Sodium Taurocholate Cotransporting Polypeptide as a Hepatitis B Virus Receptor.

    abstract:UNLABELLED:Cell culture (cc)-derived hepatitis B virus (HBV) can infect differentiated HepaRG cells, but efficient infection requires addition of polyethylene glycol (PEG) during inoculation. Identification of sodium taurocholate cotransporting polypeptide (NTCP) as an HBV receptor enabled ccHBV infection of NTCP recon...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.01153-16

    authors: Li J,Zong L,Sureau C,Barker L,Wands JR,Tong S

    更新日期:2016-08-26 00:00:00

  • Identifying the determinants in the equatorial domain of Buchnera GroEL implicated in binding Potato leafroll virus.

    abstract::Luteoviruses avoid degradation in the hemolymph of their aphid vector by interacting with a GroEL homolog from the aphid's primary endosymbiotic bacterium (Buchnera sp.). Mutational analysis of GroEL from the primary endosymbiont of Myzus persicae (MpB GroEL) revealed that the amino acids mediating binding of Potato l...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/jvi.74.10.4541-4548.2000

    authors: Hogenhout SA,van der Wilk F,Verbeek M,Goldbach RW,van den Heuvel JF

    更新日期:2000-05-01 00:00:00

  • Quasispecies of TT virus (TTV) with sequence divergence in hypervariable regions of the capsid protein in chronic TTV infection.

    abstract::Three hypervariable regions were identified in a central portion of open reading frame 1 of TT virus DNA, which codes for a putative capsid protein of 770 amino acids. TT virus circulates as quasispecies, with many amino acid substitutions in hypervariable regions, to evade immune surveillance of the hosts and to esta...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.73.11.9604-9608.1999

    authors: Nishizawa T,Okamoto H,Tsuda F,Aikawa T,Sugai Y,Konishi K,Akahane Y,Ukita M,Tanaka T,Miyakawa Y,Mayumi M

    更新日期:1999-11-01 00:00:00

  • Genome-Wide Mutagenesis of Dengue Virus Reveals Plasticity of the NS1 Protein and Enables Generation of Infectious Tagged Reporter Viruses.

    abstract::Dengue virus (DENV) is a major global pathogen that causes significant morbidity and mortality in tropical and subtropical areas worldwide. An improved understanding of the regions within the DENV genome and its encoded proteins that are required for the virus replication cycle will expedite the development of urgentl...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.01455-17

    authors: Eyre NS,Johnson SM,Eltahla AA,Aloi M,Aloia AL,McDevitt CA,Bull RA,Beard MR

    更新日期:2017-11-14 00:00:00

  • Quantitative analysis of the antiviral activity of CD8(+) T cells from human immunodeficiency virus-positive asymptomatic patients with different rates of CD4(+) T-cell decrease.

    abstract::We have measured in 22 asymptomatic human immunodeficiency virus type 1-infected patients (10 rapid progressors and 12 slow progressors) the proviral load of CD4(+) T cells homogeneously superinfected by the same dose of a non-syncytium-inducing virus in the presence or in the absence of autologous CD8(+) T cells. We ...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/jvi.74.14.6648-6651.2000

    authors: Salerno-Gonçalves R,Lu W,Andrieu JM

    更新日期:2000-07-01 00:00:00

  • VPg gene amplification correlates with infective particle formation in foot-and-mouth disease virus.

    abstract::In order to analyze the function of VPg amplification in aphthoviruses, we have undertaken the first mutational analysis of the repetitive VPg-coding region using an improved foot-and-mouth disease virus (FMDV) cDNA clone from which infective viral RNA was synthesized. A set of VPg mutants was constructed by site-dire...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.66.4.2251-2260.1992

    authors: Falk MM,Sobrino F,Beck E

    更新日期:1992-04-01 00:00:00

  • Human immunodeficiency virus type 1 coreceptors participate in postentry stages in the virus replication cycle and function in simian immunodeficiency virus infection.

    abstract::Primate lentiviruses use chemokine coreceptors in addition to the CD4 receptor to initiate virus infection. Simian immunodeficiency virus (SIV) productively infects human cells expressing CD4 and the human allele of the chemokine coreceptor CCR-5 as efficiently as it infects macaque cells expressing human CD4, suggest...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.71.5.3932-3939.1997

    authors: Chackerian B,Long EM,Luciw PA,Overbaugh J

    更新日期:1997-05-01 00:00:00

  • Cloning and analysis of integrated hepatitis virus sequences from a human hepatoma cell line.

    abstract::We report here the isolation by molecular cloning and the analysis by heteroduplex and restriction enzyme mapping of seven distinct DNA fragments containing hepatitis B virus (HBV) sequences from genomic DNA of the PLC/PRF/5 human liver carcinoma cell line (the Alexander cell). No intact full-length HBV genomes were p...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.51.3.776-787.1984

    authors: Shaul Y,Ziemer M,Garcia PD,Crawford R,Hsu H,Valenzuela P,Rutter WJ

    更新日期:1984-09-01 00:00:00

  • Mutations in classical swine fever virus NS4B affect virulence in swine.

    abstract::NS4B is one of the nonstructural proteins of classical swine fever virus (CSFV), the etiological agent of a severe, highly lethal disease of swine. Protein domain analysis of the predicted amino acid sequence of the NS4B protein of highly pathogenic CSFV strain Brescia (BICv) identified a putative Toll/interleukin-1 r...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.02050-09

    authors: Fernandez-Sainz I,Gladue DP,Holinka LG,O'Donnell V,Gudmundsdottir I,Prarat MV,Patch JR,Golde WT,Lu Z,Zhu J,Carrillo C,Risatti GR,Borca MV

    更新日期:2010-02-01 00:00:00

  • Complete genome sequence of a Newcastle disease virus strain isolated from broiler breeder flocks in China.

    abstract::In 2010 and 2011, several devastating Newcastle disease (ND) outbreaks occurred in China, affecting broilers, layers, and breeders. The CK-JSX1-201005 virus was isolated from broiler breeder flocks vaccinated with the classical ND virus (NDV) vaccine program, but laying rate decreased from 80% to 30 to 40% in the clin...

    journal_title:Journal of virology

    pub_type: 杂志文章

    doi:10.1128/JVI.02314-12

    authors: Chen F,Liu J,Liu D,Yan Z,Ji J,Qin J,Li H,Ma J,Bi Y,Xie Q

    更新日期:2012-11-01 00:00:00