Abstract:
:More than 200 open reading frames (ORFs) from the human cytomegalovirus genome have been reported as potentially coding for proteins. We have used two pattern-based in silico approaches to analyze this set of putative viral genes. With the help of an objective annotation method that is based on the Bio-Dictionary, a comprehensive collection of amino acid patterns that describes the currently known natural sequence space of proteins, we have reannotated all of the previously reported putative genes of the human cytomegalovirus. Also, with the help of MUSCA, a pattern-based multiple sequence alignment algorithm, we have reexamined the original human cytomegalovirus gene family definitions. Our analysis of the genome shows that many of the coded proteins comprise amino acid combinations that are unique to either the human cytomegalovirus or the larger group of herpesviruses. We have confirmed that a surprisingly large portion of the analyzed ORFs encode membrane proteins, and we have discovered a significant number of previously uncharacterized proteins that are predicted to be G-protein-coupled receptor homologues. The analysis also indicates that many of the encoded proteins undergo posttranslational modifications such as hydroxylation, phosphorylation, and glycosylation. ORFs encoding proteins with similar functional behavior appear in neighboring regions of the human cytomegalovirus genome. All of the results of the present study can be found and interactively explored online (http://cbcsrv.watson.ibm.com/virus/).
journal_name
J Viroljournal_title
Journal of virologyauthors
Rigoutsos I,Novotny J,Huynh T,Chin-Bow ST,Parida L,Platt D,Coleman D,Shenk Tdoi
10.1128/jvi.77.7.4326-4344.2003subject
Has Abstractpub_date
2003-04-01 00:00:00pages
4326-44issue
7eissn
0022-538Xissn
1098-5514journal_volume
77pub_type
杂志文章abstract::Kaposi's sarcoma-associated herpesvirus (KSHV) latently infects KS tumors, primary effusion lymphomas (PELs), and PEL cell lines. K12 (T0.7) is the most abundant transcript expressed in latent KSHV infection. We characterize here the K12 transcript from a PEL tumor prior to passage in cell culture. The PEL tumor KSHV ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/jvi.76.23.11880-11888.2002
更新日期:2002-12-01 00:00:00
abstract::Membrane-containing extracts isolated from tobacco plants infected with the plus-strand RNA virus, potato virus X (PVX), supported synthesis of four major, high-molecular-weight PVX RNA products (R1 to R4). Nuclease digestion and hybridization studies indicated that R1 and R2 are a mixture of partially single-stranded...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.70.7.4795-4799.1996
更新日期:1996-07-01 00:00:00
abstract::Autoradiographic analyses of deoxyribonucleic acid (DNA) synthesis in randomly growing KB cell cultures infected with equine abortion virus (EAV) suggested that viral DNA synthesis was initiated only at times that coincided with the entry of noninfected control cells into the S phase of the cell cycle. Synchronized cu...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.7.6.736-748.1971
更新日期:1971-06-01 00:00:00
abstract::Hepatitis C virus (HCV) replicates through an error-prone process that may support the evolution of genetic variants resistant to the host cell antiviral response and interferon (IFN)-based therapy. We evaluated HCV-IFN interactions within a long-term culture system of Huh7 cell lines harboring different variants of a...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.78.21.11591-11604.2004
更新日期:2004-11-01 00:00:00
abstract:UNLABELLED:Kaposi's sarcoma-associated herpesvirus (KSHV, also called human herpesvirus 8) is linked to the development of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman's disease (MCD). KSHV expresses several proteins that modulate host cell signaling pathways. One of these proteins...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00511-14
更新日期:2014-08-01 00:00:00
abstract::The enzymatic activity of recombinant influenza virus RNA polymerase is strictly dependent on the addition of a template RNA containing 5' and 3' viral sequences. Here we report the analysis of the binding specificity and physical characterization of the complex by using gel shift, modification interference, and densi...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.68.8.5108-5116.1994
更新日期:1994-08-01 00:00:00
abstract::Herpesvirus lytic DNA replication requires both the cis-acting element, the origin, and trans-acting factors, including virally encoded origin-binding protein, DNA replication enzymes, and auxiliary factors. Two lytic DNA replication origins (ori-Lyt) of Kaposi's sarcoma-associated herpesvirus (KSHV) have been identif...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01319-07
更新日期:2008-03-01 00:00:00
abstract::The unique region of the capsid protein VP1 (VP1u) of human parvovirus B19 (B19) elicits a dominant immune response and has a phospholipase A(2) (PLA(2)) activity, which is necessary for the infection. In contrast to the rest of the parvoviruses, the VP1u of B19 is thought to occupy an external position in the virion,...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01435-06
更新日期:2006-12-01 00:00:00
abstract::We studied the effect of filovirus infection on host cell gene expression by characterizing the regulation of gene expression responses in human liver cells infected with Zaire Ebolavirus (ZEBOV), Reston Ebolavirus (REBOV), and Marburgvirus (MARV), using transcriptional profiling and bioinformatics. Expression microar...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.80.6.3009-3020.2006
更新日期:2006-03-01 00:00:00
abstract::Eucaryotic, viral, and bacteriophage DNA polymerases of the alpha-like family share blocks of sequence similarity, the most conserved of which has been designated region I. Region I includes a YGDTDS motif that is almost invariant within the alpha-like family and that is similar to a motif conserved among RNA-directed...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.64.12.5883-5890.1990
更新日期:1990-12-01 00:00:00
abstract::Many replication events are involved in the influenza A virus life cycle, and they are accomplished by different virus proteins with specific functions. However, because the size of the influenza virus genome is limited, the virus uses different mechanisms to express multiple viral proteins from a single gene segment....
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.02656-12
更新日期:2013-03-01 00:00:00
abstract::The nucleic acids of influenza A, B, and C viruses were compared. Susceptibility to nucleases demonstrates that influenza C virus, just as influenza A and B viruses, possesses single-stranded RNA as its genome. The base compositions of the RNAs of influenza A, B, and influenza C virus are almost identical and comparat...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.18.2.738-744.1976
更新日期:1976-05-01 00:00:00
abstract::The Nef proteins of human immunodeficiency virus and simian immunodeficiency virus (SIV) bind the AP-1 and AP-2 clathrin adaptors to downmodulate the expression of CD4 and CD28 by recruiting them to sites of AP-2 clathrin-dependent endocytosis. Additionally, SIV Nef directly binds the CD3-zeta subunit of the CD3 compl...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/jvi.77.14.8116-8126.2003
更新日期:2003-07-01 00:00:00
abstract::The entire varicella-zoster virus (VZV) genome appears to be present in latently infected human ganglia, but the extent of virus DNA transcription is unknown. Conventional methods to study virus gene transcripts by Northern (RNA) blotting are not feasible, since ganglia are small and VZV DNA is not abundant. To circum...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.68.12.7900-7908.1994
更新日期:1994-12-01 00:00:00
abstract::Kaposi sarcoma-associated herpesvirus (KSHV) is an emerging pathogen and is the causative infectious agent of Kaposi sarcoma and two malignancies of B cell origin. To date, there is no licensed KSHV vaccine. Development of an effective vaccine against KSHV continues to be limited by a poor understanding of how the vir...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00630-19
更新日期:2019-07-30 00:00:00
abstract::To determine mechanisms by which persistent viral infections are established and maintained, we initiated persistent infections of murine erythroleukemia (MEL) cells by using reovirus strains type 3 Abney and type 3 Dearing. Establishment of persistent reovirus infections of MEL cells was not associated with a signifi...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.71.1.299-306.1997
更新日期:1997-01-01 00:00:00
abstract::Whether a genetic informational nucleic acid is required for the infectivity of transmissible spongiform encephalopathies is central to the debate about the infectious agent. Here we report that an infectious prion formed with bacterially expressed recombinant prion protein plus synthetic polyriboadenylic acid and syn...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.06216-11
更新日期:2012-02-01 00:00:00
abstract::Meq is the major Marek's disease virus (MDV)-encoded oncoprotein and is essential for T-cell lymphomagenesis. Meq and several noncoding RNAs, including three microRNA (MiR) clusters, are expressed from the repeats of the MDV genome during latent infection of T cells. To investigate the state of the chromatin in this a...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.06113-11
更新日期:2012-02-01 00:00:00
abstract::BCX 2798 (4-azido-5-isobutyrylamino-2,3-didehydro-2,3,4,5-tetradeoxy-d-glycero-d-galacto-2-nonulopyranosic acid) effectively inhibited the activities of the hemagglutinin-neuraminidase (HN) of human parainfluenza viruses (hPIV) in vitro and protected mice from lethal infection with a recombinant Sendai virus whose HN ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00474-08
更新日期:2008-09-01 00:00:00
abstract::Immature retroviral particles are assembled by self-association of the structural polyprotein precursor Gag. During maturation the Gag polyprotein is proteolytically cleaved, yielding mature structural proteins, matrix (MA), capsid (CA), and nucleocapsid (NC), that reassemble into a mature viral particle. Proteolytic ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.05564-11
更新日期:2012-02-01 00:00:00
abstract::Homo-oligomeric runs were inserted into a spleen necrosis virus-based retrovirus vector to determine the nature and rate of mutations within runs of 10 to 12 identical nucleotides during a single replication cycle. Clones of helper cells containing integrated copies of retroviral vectors were used to produce virus for...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.68.7.4196-4203.1994
更新日期:1994-07-01 00:00:00
abstract::Enveloped viruses often require cleavage of a surface glycoprotein by a cellular endoprotease such as furin for infectivity and virulence. Previously, we showed that Ebola virus glycoprotein does not require the furin cleavage motif for virus replication in cell culture. Here, we show that there are no appreciable dif...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.02486-06
更新日期:2007-03-01 00:00:00
abstract::Initial studies determined whether intraperitoneal (i.p.) injection of BALB/c mice with 0.1, 1.0, and 10 mg of adriamycin (a cardiotoxic anthracycline antibiotic) for times ranging between 1 and 9 weeks prior to i.p. injection of 10(5) PFU of coxsackievirus B3 (CVB3) would alter the severity of virus-induced myocardit...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.66.11.6541-6546.1992
更新日期:1992-11-01 00:00:00
abstract::Structural differences between human leukocyte virus-induced interferon and human fibroblast polyinosinic-polycytidylic acid (rIn-rCn)-induced interferon have been noted in previous studies. This study reports the behavior of human leukocyte and fibroblast interferon, induced by virus and by rIn-rCn, in several lectin...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.16.5.1124-1130.1975
更新日期:1975-11-01 00:00:00
abstract::The full repertoire of hepatitis B virus (HBV) peptides that bind to the common HLA class I molecules found in areas with a high prevalence of chronic HBV infection has not been determined. This information may be useful for designing immunotherapies for chronic hepatitis B. We identified amino acid residues under pos...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01471-09
更新日期:2010-01-01 00:00:00
abstract::Feline panleukopenia virus (FPV) and its host range variant, canine parvovirus (CPV), can bind the feline transferrin receptor (TfR), while only CPV binds to the canine TfR. Introducing two CPV-specific changes into FPV (at VP2 residues 93 and 323) endowed that virus with the canine TfR binding property and allowed ca...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/jvi.77.18.10099-10105.2003
更新日期:2003-09-01 00:00:00
abstract::The Epstein-Barr virus (EBV) BMRF1 protein is a DNA polymerase processivity factor. We have deleted the BMRF1 open reading frame from the EBV genome and assessed the DeltaBMRF1 EBV phenotype. DeltaBMRF1 viruses were replication deficient, but the wild-type phenotype could be restored by BMRF1 trans-complementation. Th...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.80.10.5078-5081.2006
更新日期:2006-05-01 00:00:00
abstract::Recombination is one of the driving forces of viral evolution. RNA recombination events among similar RNA viruses are frequent, although RNA recombination could also take place among unrelated viruses. In this paper, we have established efficient interviral recombination systems based on yeast and plants. We show that...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01015-19
更新日期:2019-12-12 00:00:00
abstract::Using less stringent hybridization conditions and cloned viral DNA probes representing the avian sarcoma virus gag, pol, env, and long terminal repeat (LTR) gene sequences, we detected related sequences in two avian species purportedly lacking all endogenous avian leukosis viruses, the ev- chicken and the Japanese qua...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.59.3.669-675.1986
更新日期:1986-09-01 00:00:00
abstract::A herpes simplex virus type 1 variant [C239(TK-)] harboring a deletion in the thymidine kinase (TK) gene was assessed for capacity to establish latent infections. Outbred Swiss Webster mice were inoculated on both hind footpads, and numbers of neurons expressing latency-associated transcript and amounts of viral DNA i...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.63.11.4976-4978.1989
更新日期:1989-11-01 00:00:00