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RNA Genome (rna + genome)
Selected AbstractsInfluenza virus RNA polymerase PA subunit is a novel serine protease with Ser624 at the active siteGENES TO CELLS, Issue 2 2001Koyu Hara Background Influenza virus RNA polymerase is a multifunctional enzyme that catalyses both transcription and replication of the RNA genome. The function of the influenza virus RNA polymerase PA subunit in viral replication is poorly understood, although the enzyme is known to be required for cRNA , vRNA synthesis. The protease related activity of PA has been discussed ever since protease-inducing activity was demonstrated in transfection experiments. Results PA protein was highly purified from insect cells infected with the recombinant baculovirus carrying PA cDNA, and a novel chymotrypsin-type serine protease activity was identified with the synthetic peptide, Suc-LLVY-MCA, in the PA protein. [3H]DFP was crosslinked with PA and a mutational analysis revealed that serine624 was as an active site for the protease activity. Conclusions These results constitute the demonstration of protease activity in PA subunit of the influenza virus RNA polymerase complexes. [source] Effects of HCV proteins in current HCV transgenic modelsHEPATOLOGY RESEARCH, Issue 2 2010Jian Jiao Hepatits C virus (HCV) is an enveloped virus with positive-sense single-stranded RNA genome that causes both acute and persistent infections associated with chronic hepatitis, cirrhosis and hepatocellular carcinoma, which needs fully functional human hepatocytes for its development. Due to the strict human tropism of HCV, only human and higher primates such as chimpanzees have been receptive to HCV infection and development, cognition about pathophysiololgy and host immune responses of HCV infection is limited by lacking of simple laboratory models of infection for a long time. During the past decade, gene transfer approaches have been helpful to the understanding of the molecular basis of human disease. Transgenic cell lines, chimeric and transgenic animal models were developed and had been demonstrated their invaluable benefits. This review focuses on the existing HCV transgenic models and summarize the relative results about probable pathophysical changes induced by HCV proteins. [source] Transcriptional inactivation of amphotropic murine leukemia virus replication in human cellsJOURNAL OF MEDICAL VIROLOGY, Issue 2 2003Martin Ploss Abstract Amphotropic murine leukemia virus (MLV) replicates in cells from various mammalian species including humans and is a potential contaminant in MLV vector preparations for human gene transfer studies. Because MLV replication proceeds through an RNA genome that is generated under the control of viral enhancer and promoter elements, vectors were developed that delete such elements during transduction to reduce the generation of replication-competent virus. It was shown recently that replication of amphotropic MLV in certain human cells is possible without the 75 bp transcription enhancers. It is now demonstrated that enhancer-independent replication requires functional elements within U3 and is repressed by an extended deletion in the U3 region comprising enhancers, promoter and flanking sequences. It is concluded that the transcriptional inactivation of amphotropic MLV in human cells requires the combined deletion of enhancers and of additional elements in U3. J. Med. Virol. 69:267,272, 2003. © 2003 Wiley-Liss, Inc. [source] Pepino mosaic virus: a successful pathogen that rapidly evolved from emerging to endemic in tomato cropsMOLECULAR PLANT PATHOLOGY, Issue 2 2010INGE M. HANSSEN SUMMARY Taxonomy:Pepino mosaic virus (PepMV) belongs to the Potexvirus genus of the Flexiviridae family. Physical properties: PepMV virions are nonenveloped flexuous rods that contain a monopartite, positive-sense, single-stranded RNA genome of 6.4 kb with a 3, poly-A tail. The genome contains five major open reading frames (ORFs) encoding a 164-kDa RNA-dependent RNA polymerase (RdRp), three triple gene block proteins of 26, 14 and 9 kDa, and a 25-kDa coat protein. Genome diversity: Four PepMV genotypes, with an intergenotype RNA sequence identity ranging from 78% to 95%, can be distinguished: the original Peruvian genotype (LP); the European (tomato) genotype (EU); the American genotype US1; and the Chilean genotype CH2. Transmission: PepMV is very efficiently transmitted mechanically, and a low seed transmission rate has been demonstrated. In addition, bumblebees have been associated with viral transmission. Host range: Similar to other Potexviruses, PepMV has a rather narrow host range that is thought to be largely restricted to species of the Solanaceae family. After originally being isolated from pepino (Solanum muricatum), PepMV has been identified in natural infections of the wild tomato species S. chilense, S. chmielewskii, S. parviflorum and S. peruvianum. PepMV is causing significant problems in the cultivation of the glasshouse tomato Solanum lycopersicum, and has been identified in weeds belonging to various plant families in the vicinity of tomato glasshouses. Symptomatology: PepMV symptoms can be very diverse. Fruit marbling is the most typical and economically devastating symptom. In addition, fruit discoloration, open fruit, nettle-heads, leaf blistering or bubbling, leaf chlorosis and yellow angular leaf spots, leaf mosaic and leaf or stem necrosis have been associated with PepMV. The severity of PepMV symptoms is thought to be dependent on environmental conditions, as well as on the properties of the viral isolate. Minor nucleotide sequence differences between isolates from the same genotype have been shown to lead to enhanced aggressiveness and symptomatology. Control: Prevention of infection through strict hygiene measures is currently the major strategy for the control of PepMV in tomato production. Cross-protection can be effective, but only under well-defined and well-controlled conditions, and the effectiveness depends strongly on the PepMV genotype. [source] Mammalian reovirus core protein,µ2 initiates at the first start codon and is acetylatedRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 24 2002Magdalena I. Swanson Mammalian reovirus is an enteric virus that contains a double-stranded RNA genome. The genome consists of ten RNA segments that encode eight structural and three non-structural proteins. The structural proteins form a double-layered structure. The innermost layer, called the core, consists of five proteins (,1, ,2, ,3, µ2, and ,2). Protein ,3 is the RNA-dependent RNA polymerase (RdRp) and µ2 is thought to be an RdRp cofactor. Translation of most reovirus proteins is known to commence at the first start codon. However, the translation initiation site of the viral core protein,µ2, encoded by the M1 RNA segment, has been in dispute. Although the theoretical molecular weight of µ2 is 83 267,Da the actual molecular weight is unknown because,µ2 runs aberrantly in SDS-PAGE and has resisted characterization by Edman degradation, indicating that the amino terminus is post-translationally modified. In this study, we used proteolysis coupled with MALDI-Qq-TOFMS to determine that translation of µ2 initiates at the first AUG codon, that its actual molecular weight approximates the theoretical value of 83,kDa, that the amino terminal methionine residue is removed, and that the next amino acid (alanine) is post-translationally acetylated. Copyright © 2002 John Wiley & Sons, Ltd. [source] Two Subgroups of Stapes Fixation: Otosclerosis and Pseudo-Otosclerosis,THE LARYNGOSCOPE, Issue 11 2005Tamás Karosi MD Abstract Hypothesis: Stapes ankylosis is a disease with variable histopathology and can be caused by otosclerosis or pseudo-otosclerosis. Viral pathogenesis of otosclerosis could be established only by correlative analysis: histologic examination of the stapes footplate and reverse-transcriptase polymerase chain reaction (RT-PCR) amplification of the viral RNA. Background: Presence of the RNA genome of measles virus was demonstrated in the footplates of clinically otosclerotic patients by RT-PCR, and also viral proteins were detected by immunohistochemistry. Methods: Nucleic acids were extracted from ankylotic stapes footplates of clinically stapes fixation patients (n = 104). Measles virus genomic nucleoprotein (NP) RNA was amplified by seminested RT-PCR. Amplification results were correlated to postoperative histologic and audiologic findings. Results: Measles virus RNA was detectable only in histologically otosclerotic stapes footplates (n = 67). Histology for virus negative footplates (n = 37) excluded otosclerosis. Virus negative stapes footplates showed nonotosclerotic, degenerative disorders. Conclusions: Stapes ankylosis is a heterogeneous disease causing conductive hearing loss with different etiologies. Nonotosclerotic stapes fixations could be established as pseudo-otosclerosis and may belong to nonspecific, degenerative disorders with variable and noncharacteristic histopathology. Otosclerosis is an inflammatory disease caused by persisting measles virus infection of the otic cap-sule. [source] Crystallization and preliminary X-ray analysis of the human respiratory syncytial virus nucleocapsid proteinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2008K. El Omari Human respiratory syncytial virus (HRSV) has a nonsegmented negative-stranded RNA genome which is encapsidated by the HRSV nucleocapsid protein (HRSVN) that is essential for viral replication. HRSV is a common cause of respiratory infection in infants, yet no effective antiviral drugs to combat it are available. Recent data from an experimental anti-HRSV compound, RSV-604, indicate that HRSVN could be the target site for drug action. Here, the expression, purification and preliminary data collection of decameric HRSVN as well as monomeric N-terminally truncated HRSVN mutants are reported. Two different crystal forms of full-length selenomethionine-labelled HRSVN were obtained that diffracted to 3.6 and ,5,Å resolution and belonged to space group P212121, with unit-cell parameters a = 133.6, b = 149.9, c = 255.1,Å, and space group P21, with unit-cell parameters a = 175.1, b = 162.6, c = 242.8,Å, , = 90.1°, respectively. For unlabelled HRSVN, only crystals belonging to space group P21 were obtained that diffracted to 3.6,Å. A self-rotation function using data from the orthorhombic crystal form confirmed the presence of tenfold noncrystallographic symmetry, which is in agreement with a reported electron-microscopic reconstruction of HRSVN. Monomeric HRSVN generated by N-terminal truncation was designed to assist in structure determination by reducing the size of the asymmetric unit. Whilst such HRSVN mutants were monomeric in solution and crystallized in a different space group, the size of the asymmetric unit was not reduced. [source] The ins and outs of HIV replicationCELLULAR MICROBIOLOGY, Issue 5 2005Candace Gomez Summary The life cycle of HIV-1 involves a series of steps necessary for the successful infection of human target cells. First the RNA genome enters the cytoplasm after the fusion of the viral membrane and that of the target cell. The RNA genome is then converted to DNA form through the process of reverse transcription. The DNA genome is then integrated into the host cell DNA. Next, viral proteins and more copies of the viral genome are produced. These components assemble to form new virions that are then able to propagate. The cellular proteins involved in HIV-1 entry have been known for more than a decade now and the study of the cellular and viral components involved in HIV-1 entry has led to the development of many therapeutic strategies and drugs designed to block viral replication. Recently, there have been significant advances in the understanding of HIV-1 assembly as a consequence of the identification of the cellular factors that mediate this process. This review will provide a basic outline of the current understanding of HIV-1 entry and exit. [source] Real-time polymerase chain reaction as a rapid and efficient alternative to estimation of picornavirus titers by tissue culture infectious dose 50% or plaque forming unitsMICROBIOLOGY AND IMMUNOLOGY, Issue 3 2009Nina Jonsson ABSTRACT Quantification of viral infectious units is traditionally measured by methods based on forming plaques in semisolid media (PFU) or endpoint dilution of a virus-containing solution (TCID50), methods that are laborious, time-consuming and take on average 3,7 days to carry out. Quantitative real-time PCR is an established method to quantify nucleic acids at high accuracy and reproducibility, routinely used for virus detection and identification. In the present study, a procedure was developed using a two-step real-time PCR and the SYBR Green detection method to study whether there are correlations between TCID50/ml, PFU/ml and Ct values generated by real-time PCR enabling rapid and efficient calculation of titer equivalents when working with viruses in the research laboratory. In addition, an external standard with known concentrations was included using in vitro transcribed viral RNA, thus allowing the calculation of the amount of RNA copies needed for various applications (i.e. per plaque or TCID50). The results show that there is a correlation between the three quantification methods covering a wide range of concentration of viruses. Furthermore, a general regression line between TCID50 and Ct values was obtained for all viruses included in the study, which enabled recording titer equivalents using real-time PCR. Finally, by including an external standard, the amount of RNA genomes generating one TCID50 or PFU for each enterovirus serotype included was determined. [source] RNA commutes to work: regulation of plant gene expression by systemically transported RNA moleculesBIOESSAYS, Issue 12 2001Shoko Ueki Although long-distance movement of endogenous mRNAs in plants is well established, the functional contributions of these transported RNA molecules has remained unclear. In a recent report, Kim et al.2001 showed that systemically transported mRNA is capable of causing phenotypic change in developing tissue. Here, this finding and its significance are reviewed and discussed in detail. In addition, in order to give proper perspective, long-distance transport of other types of RNAs, e.g., RNA elicitors of post-transcriptional gene silencing and RNA genomes of plant viruses, and its possible regulation are discussed. BioEssays 23:1087,1090, 2001. © 2001 John Wiley & Sons, Inc. 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