Home About us Contact
|
Home About us Contact | ||
|
|
||
RNA Viruses (rna + viruse)
Kinds of RNA Viruses Selected AbstractsA new and efficient method for inhibition of RNA viruses by DNA interferenceFEBS JOURNAL, Issue 16 2009Monika Nowak We report here a new method for inhibition of RNA viruses induced by dsDNA. We demonstrated that both long dsDNA molecules and short interfering DNA with a sequence complementary to that of viral RNA inhibited tobacco mosaic virus expression and prevented virus spread. Also, the expression of the HIV-1 gp41 gene in HeLa cells was inhibited by complementary short interfering DNA. We showed that Dicer processed dsDNA, which suggests activation of the cellular machinery involved in silencing of RNA. For the silencing of viral RNA effected with dsDNA, we coined the term DNA interference technology. [source] Paternal sex in parthenogenetic planarians: a tool to investigate the accumulation of deleterious mutationsJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 1 2000Storhas Clonally reproducing organisms are expected to accumulate slightly deleterious mutations, and this has been demonstrated in RNA viruses, bacteria and unicellular algae. In this paper we present evidence for increased embryo mortality in obligate parthenogenetic strains of the freshwater flatworm Schmidtea polychroa, possibly indicating the action of deleterious mutations. The inheritance of this fitness defect was tested by crossing parthenogens with sexuals. This is possible because both forms are simultaneous hermaphrodites that produce fertile sperm. The resulting sexual offspring showed significantly increased embryo mortality in comparison to offspring of a sexual × sexual cross. Alternatives to a mutation explanation of these results, like the degeneration of male traits in parthenogens, are being discussed. In conclusion, these results lend support to the hypothesis that sex is advantageous to a multicellular organism because it prevents the accumulation of deleterious mutations. [source] Evaluation and application of reverse transcription loop-mediated isothermal amplification for detection of noroviruses,JOURNAL OF MEDICAL VIROLOGY, Issue 3 2007Tomoko Yoda Abstract A one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of norovirus (NV) was developed. In order to design primer sets for the detection of a wide range of NVs, NVs were categorized into three groups, that is, genogroup I (GI), prevalent GII, and minor GII; three sets of primers were developed for each group. Clinical specimens of patients suffering from enteric RNA viruses, such as NV, group A and C rotavirus, and sapovirus were examined using these primer sets. Various genotypes of NVs were detected in clinical specimens from patients infected with NV where no false positive reaction was observed with other enteric RNA viruses. Additionally, 88 samples of acute gastroenteritis outbreaks were analyzed by an RT-LAMP assay and compared with the results of routine RT-PCR. The results of the RT-LAMP assay corresponded well to that of RT-PCR. These findings suggest the practical application of the RT-LAMP assay for the detection of NVs in clinical specimens. Consequently, the RT-LAMP system and conventional detection kits (NVGI and NVGII detection kits; Eiken Chemical Co., Ltd., Japan) were compared. The detection rate of the prevalent and minor GII primer sets was similar to that of the conventional NVGII kit, while the detection rate of the GI primer set is different because it can detect several genotypes better than the conventional NVGI kit. This is an initial report that the RT-LAMP system is able to detect NVs in clinical specimens within a wide range. J. Med. Virol. 79:326,334, 2007. © 2007 Wiley-Liss, Inc. [source] Expression of the hepatitis C virus structural proteins in mammalian cells induces morphology similar to that in natural infectionJOURNAL OF VIRAL HEPATITIS, Issue 1 2002S. J. Greive Like many positive-strand RNA viruses, replication of the hepatitis C virus (HCV) is associated with cytoplasmic membrane rearrangements. However, it is unclear which HCV proteins induce these ultrastructural features. This work examined the morphological changes induced by expression of the HCV structural proteins, core, E1 and E2, expressed from a Semliki Forest Virus (SFV) recombinant RNA replicon. Electron microscopy of cells expressing these proteins showed cytoplasmic vacuoles containing membranous and electron-dense material that were distinct from the type I cytoplasmic vacuoles induced during SFV replicon replication. Immunogold labelling showed that the core and E2 proteins localized to the external and internal membranes of these vacuoles, but at times were also associated with some of the internal amorphous material. Dual immunogold labelling with antibodies raised against the core protein and against an endoplasmic reticulum (ER)-resident protein (protein disulphide isomerase) showed that the HCV-induced vacuoles were associated with ER-labelled membranes. This report has identified an association between the HCV core and E2 proteins with induced cytoplasmic vacuoles which are morphologically similar to those observed in HCV-infected liver tissue, suggesting that the HCV structural proteins may be responsible for the induction of these vacuoles during HCV replication in vivo. [source] Genetic variability: The key problem in the prevention and therapy of RNA-based virus infectionsMEDICINAL RESEARCH REVIEWS, Issue 4 2003Magdalena Figlerowicz Abstract Despite extraordinary progress that has recently been made in biomedical sciences, viral infectious diseases still remain one of the most serious world health problems. Among the different types of viruses, those using RNA as their genetic material (RNA viruses and retroviruses) are especially dangerous. At present there is no medicine allowing an effective treatment of RNA-based virus infections. Many RNA viruses and retroviruses need only a few weeks to escape immune response or to produce drug-resistant mutants. This seems to be the obvious consequence of the unusual genetic variability of RNA-based viruses. An individual virus does not form a homogenous population but rather a set of similar but not identical variants. In consequence, RNA-based viruses can easily adapt to environmental changes, also those resulting from immune system response or therapy. The modifications identified within viral genes can be divided into two groups: point mutations and complex genome rearrangements. The former arises mainly during error-prone replication, whereas RNA recombination and generic reassortment are responsible for the latter. This article shortly describes major strategies used to control virus infections. Then, it presents the various mechanisms generating the genetic diversity of RNA-based viruses, which are most probably the main cause of clinical problems. © 2003 Wiley Periodicals, Inc. Med Res Rev, 23, No. 4, 488,518, 2003 [source] Tobraviruses,plant pathogens and tools for biotechnologyMOLECULAR PLANT PATHOLOGY, Issue 4 2010STUART A. MACFARLANE SUMMARY The tobraviruses, Tobacco rattle virus (TRV), Pea early-browning virus (PEBV) and Pepper ringspot virus (PepRSV), are positive-strand RNA viruses with rod-shaped virus particles that are transmitted between plants by trichodorid nematodes. As a group, these viruses infect many plant species, with TRV having the widest host range. Recent studies have begun to dissect the interaction of TRV with potato, currently the most commercially important crop disease caused by any of the tobraviruses. As well as being successful plant pathogens, these viruses have become widely used as vectors for expression in plants of nonviral proteins or, more frequently, as initiators of virus-induced gene silencing (VIGS). Precisely why tobraviruses should be so effective as VIGS vectors is not known; however, molecular studies of the mode of action of the tobravirus silencing suppressor protein are shedding some light on this process. [source] Beet yellows virus: the importance of being differentMOLECULAR PLANT PATHOLOGY, Issue 2 2003Valerian V. Dolja SUMMARY Taxonomic relationship: Type member of the genus Closterovirus, family Closteroviridae. A member of the alphavirus-like supergroup of positive-strand RNA viruses. Physical properties: Virions are flexuous filaments of ,1300 nm in length and ,12 nm in diameter that are made up of a ,15.5 kb RNA and five proteins. The major capsid protein forms virion body of helical symmetry that constitutes ,95% of the virion length. The short virion tail is assembled by the minor capsid protein, Hsp70-homologue, ,64-kDa protein, and ,20-kDa protein. Viral proteins: The 5,-most ORFs 1a and 1b encode leader proteinase and RNA replicase. The remaining ORFs 2,8 are expressed by subgenomic mRNAs that encode 6-kDa membrane protein, Hsp70 homologue, ,64-kDa protein, minor and major capsid proteins, ,20-kDa protein, and ,21-kDa protein, respectively. Hosts: The principal crop plants affected by Beet yellows virus (BYV) are sugar beet (Beta vulgaris) and spinach (Spinacea oleracea). In addition, BYV was reported to infect ,120 species in 15 families. Most suitable propagation species are Nicotiana benthamiana, Tetragonia expansa, and Claytonia perfoliata. [source] Plant virus infection-induced persistent host gene downregulation in systemically infected leavesTHE PLANT JOURNAL, Issue 2 2008Zoltán Havelda Summary Understanding of virus infection-induced alterations in host plant gene expression and metabolism leading to the development of virus disease symptoms is both scientifically and economically important. Here, we show that viruses belonging to various RNA virus families are able to induce efficient host gene mRNA downregulation (shut-off) in systemically infected leaves. We demonstrate that the host gene mRNA shut-off overlaps spatially with virus-occupied sectors, indicating the direct role of virus accumulation in this phenomenon. The establishment of shut-off was not directly connected to active viral replication or the RNA-silencing machinery. Importantly, the induced shut-off phenomenon persisted for several weeks, resulting in severe deficiency of mRNA for important housekeeping genes in the infected plants. Interestingly, we found that some other RNA viruses do not induce or only slightly induce the shut-off phenomenon for the same set of genes, implicating genetic determination in this process. Nuclear run-on experiments suggest that plant viruses, similarly to animal viruses, mediate suppression of host mRNA synthesis in the nucleus. By investigating various host,virus interactions, we revealed a correlation between the intensity of the shut-off phenomenon and the severity of disease symptoms. Our data suggest that efficient and persistent downregulation of host genes may be an important component of symptom development in certain host,virus interactions. [source] Structure of the C-terminal domain of nsp4 from feline coronavirusACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2009Ioannis Manolaridis Coronaviruses are a family of positive-stranded RNA viruses that includes important pathogens of humans and other animals. The large coronavirus genome (26,31,kb) encodes 15,16 nonstructural proteins (nsps) that are derived from two replicase polyproteins by autoproteolytic processing. The nsps assemble into the viral replication,transcription complex and nsp3, nsp4 and nsp6 are believed to anchor this enzyme complex to modified intracellular membranes. The largest part of the coronavirus nsp4 subunit is hydrophobic and is predicted to be embedded in the membranes. In this report, a conserved C-terminal domain (,100 amino-acid residues) has been delineated that is predicted to face the cytoplasm and has been isolated as a soluble domain using library-based construct screening. A prototypical crystal structure at 2.8,Å resolution was obtained using nsp4 from feline coronavirus. Unmodified and SeMet-substituted proteins were crystallized under similar conditions, resulting in tetragonal crystals that belonged to space group P43. The phase problem was initially solved by single isomorphous replacement with anomalous scattering (SIRAS), followed by molecular replacement using a SIRAS-derived composite model. The structure consists of a single domain with a predominantly ,-helical content displaying a unique fold that could be engaged in protein,protein interactions. [source] Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 proteinACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2003Valérie Campanacci The aetiologic agent of the recent epidemics of Severe Acute Respiratory Syndrome (SARS) is a positive-stranded RNA virus (SARS-CoV) belonging to the Coronaviridae family and its genome differs substantially from those of other known coronaviruses. SARS-CoV is transmissible mainly by the respiratory route and to date there is no vaccine and no prophylactic or therapeutic treatments against this agent. A SARS-CoV whole-genome approach has been developed aimed at determining the crystal structure of all of its proteins or domains. These studies are expected to greatly facilitate drug design. The genomes of coronaviruses are between 27 and 31.5,kbp in length, the largest of the known RNA viruses, and encode 20,30 mature proteins. The functions of many of these polypeptides, including the Nsp9,Nsp10 replicase-cleavage products, are still unknown. Here, the cloning, Escherichia coli expression, purification and crystallization of the SARS-CoV Nsp9 protein, the first SARS-CoV protein to be crystallized, are reported. Nsp9 crystals diffract to 2.8,Å resolution and belong to space group P61/522, with unit-cell parameters a = b = 89.7, c = 136.7,Å. With two molecules in the asymmetric unit, the solvent content is 60% (VM = 3.1,Å3,Da,1). [source] Intraclonal variation in RNA viruses: generation, maintenance and consequencesBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2003SANTIAGO F. ELENA This paper explores the evolutionary implications of the enormous variability that characterizes populations of RNA viruses and retroviruses. It begins by examining the magnitude of genetic variation in both natural and experimental populations. In natural populations, differences arise even within individual infected patients, with the per-site nucleotide diversity at this level ranging from < 1% to 6%. In laboratory populations, two viruses sampled from the same clone differed by ,0.7% in their fitness. Three different mechanisms that may be important in maintaining viral genetic variability were tested: (1) Fisher's fundamental theorem, to compare the observed rate of fitness change with the extent of fitness-related variation within the same experimental populations; (2) magnitude of genomic mutation rate, to assess whether it correlated with fitness-related variation, as predicted by the mutation-selection balance hypothesis; (3) frequency-dependent selection, which affords rare genotypes an advantage. The paper concludes with a discussion of two evolutionary consequences of variability: the fixation of deleterious mutations by drift in small populations and the role of clonal interference in large ones. © 2003 The Linnean Society of London. Biological Journal of the Linnean Society, 2003, 79, 17,26. [source] Purification, crystallization and preliminary X-ray crystallographic analysis of the nucleocapsid protein of Bunyamwera virusACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2006Qingxian Zhou Bunyamwera virus (BUNV) is the prototypic member of the Bunyaviridae family of segmented negative-sense RNA viruses. The BUNV nucleocapsid protein has been cloned and expressed in Escherichia coli. The purified protein has been crystallized and a complete data set has been collected to 3.3,Å resolution at a synchrotron source. Crystals of the nucleocapsid protein belong to space group C2, with unit-cell parameters a = 384.7, b = 89.8, c = 89.2,Å, , = 94.4°. Self-rotation function analysis of the X-ray diffraction data has provided insight into the oligomeric state of the protein as well as the orientation of the oligomers in the asymmetric unit. The structure determination of the protein is ongoing. [source] Expression, purification and crystallization of the SARS-CoV macro domainACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2006Hélène Malet Macro domains or X domains are found as modules of multidomain proteins, but can also constitute a protein on their own. Recently, biochemical and structural studies of cellular macro domains have been performed, showing that they are active as ADP-ribose-1,,-phosphatases. Macro domains are also present in a number of positive-stranded RNA viruses, but their precise function in viral replication is still unknown. The major human pathogen severe acute respiratory syndrome coronavirus (SARS-CoV) encodes 16 non-structural proteins (nsps), one of which (nsp3) encompasses a macro domain. The SARS-CoV nsp3 gene region corresponding to amino acids 182,355 has been cloned, expressed in Escherichia coli, purified and crystallized. The crystals belong to space group P21, with unit-cell parameters a = 37.5, b = 55.6, c = 108.9,Å, , = 91.4°, and the asymmetric unit contains either two or three molecules. Both native and selenomethionine-labelled crystals diffract to 1.8,Å. [source] Qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirusCELLULAR MICROBIOLOGY, Issue 6 2010Mustafa Ulasli Summary Coronaviruses (CoV) are enveloped positive-strand RNA viruses that induce different membrane rearrangements in infected cells in order to efficiently replicate and assemble. The origin, the protein composition and the function of these structures are not well established. To shed further light on these structures, we have performed a time-course experiment in which the mouse hepatitis virus (MHV)-induced membrane rearrangements were examined qualitatively and quantitatively by (immuno)-electron microscopy. With our approach we were able to confirm the appearance of 6, previously reported, membranous structures during the course of a complete infection cycle. These structures include the well-characterized double-membrane vesicles (DMVs), convoluted membranes (CMs) and virions but also the more enigmatic large virion-containing vacuoles (LVCVs), tubular bodies (TBs) and cubic membrane structures (CMSs). We have characterized the LVCVs, TBs and CMSs, and found that the CoV-induced structures appear in a strict order. By combining these data with quantitative analyses on viral RNA, protein synthesis and virion release, this study generates an integrated molecular and ultrastructural overview of CoV infection. In particular, it provides insights in the role of each CoV-induced structure and reveals that LVCVs are ERGIC/Golgi compartments that expand to accommodate an increasing production of viral particles. [source] The ESCRT machinery is not required for human cytomegalovirus envelopmentCELLULAR MICROBIOLOGY, Issue 12 2007Alberto Fraile-Ramos Summary The human cytomegalovirus (HCMV) has been proposed to complete its final envelopment on cytoplasmic membranes prior to its release to the extracellular medium. The nature of these membranes and the mechanisms involved in virus envelopment and release are poorly understood. Here we show by immunogold-labelling and electron microscopy that CD63, a marker of multivesicular bodies (MVBs), is incorporated into the viral envelope, supporting the notion that HCMV uses endocytic membranes for its envelopment. We therefore investigated a possible role for the cellular endosomal sorting complex required for transport (ESCRT) machinery in HCMV envelopment. Depletion of tumour suppressor gene 101 and ALIX/AIP1 with small interfering RNAs (siRNAs) in HCMV-infected cells did not affect virus production. In contrast, siRNAs against the vacuolar protein sorting 4 (VPS4) proteins silenced the expression of VPS4A and VPS4B, inhibited the sorting of epidermal growth factor to lysosomes, the formation of HIV Gag-derived virus-like particles and vesicular stomatitis virus infection, but enhanced the number of HCMV viral particles produced. Treatment of infected cells with protease inhibitors also increased viral production. These studies indicate that, in contrast to some enveloped RNA viruses, HCMV does not require the cellular ESCRT machinery to complete its envelopment. [source] IFN, induction by influenza A virus is mediated by RIG-I which is regulated by the viral NS1 proteinCELLULAR MICROBIOLOGY, Issue 4 2007Bastian Opitz Summary Influenza A virus causes epidemics of respiratory diseases in humans leading to thousands of death annually. One of its major virulence factors, the non-structural protein 1 (NS1), exhibits interferon-antagonistic properties. While epithelial cells of the respiratory tract are the primary targets of influenza virus, the virus-sensing mechanisms in these cells eventually leading to IFN, production are incompletely understood. Here we show that infection of epithelial cells with NS1-deficient influenza A virus upregulated expression of two molecules that have been previously implicated in sensing of RNA viruses, the retinoic acid-inducible gene I (RIG-I) and the melanoma differentiation-associated gene 5 (MDA5). Gene silencing and overexpression experiments demonstrated that RIG-I, its adapter interferon-beta promoter stimulator 1 (IPS-1) and interferon-regulated factor 3 (IRF3) were involved in influenza A virus-mediated production of the antiviral IFN,. In addition, we showed that the NS1 protein is capable to inhibit the RIG-I-induced signalling, a mechanism which corresponded to the observation that only NS1-deficient but not the wild-type virus induced high-level production of IFN,. In conclusion, we demonstrated a critical involvement of RIG-I, IPS-1 and IRF3 in influenza A virus infection of epithelial cells. [source] Ringing the alarm bells: signalling and apoptosis in influenza virus infected cellsCELLULAR MICROBIOLOGY, Issue 3 2006Stephan Ludwig Summary Small RNA viruses such as influenza viruses extensively manipulate host-cell functions to support their replication. At the same time the infected cell induces an array of defence mechanisms to fight the invader. These processes are mediated by a variety of intracellular signalling cascades. Here we will review the current knowledge of functional kinase signalling and apoptotic events in influenza virus infected cells and how these viruses have learned to misuse these cellular responses for efficient replication. [source] Nucleic acid sensing receptors in systemic lupus erythematosus: development of novel DNA- and/or RNA-like analogues for treating lupusCLINICAL & EXPERIMENTAL IMMUNOLOGY, Issue 2 2010P. Lenert Summary Double-stranded (ds) DNA, DNA- or RNA-associated nucleoproteins are the primary autoimmune targets in SLE, yet their relative inability to trigger similar autoimmune responses in experimental animals has fascinated scientists for decades. While many cellular proteins bind non-specifically negatively charged nucleic acids, it was discovered only recently that several intracellular proteins are involved directly in innate recognition of exogenous DNA or RNA, or cytosol-residing DNA or RNA viruses. Thus, endosomal Toll-like receptors (TLR) mediate responses to double-stranded RNA (TLR-3), single-stranded RNA (TLR-7/8) or unmethylated bacterial cytosine (phosphodiester) guanine (CpG)-DNA (TLR-9), while DNA-dependent activator of IRFs/Z-DNA binding protein 1 (DAI/ZBP1), haematopoietic IFN-inducible nuclear protein-200 (p202), absent in melanoma 2 (AIM2), RNA polymerase III, retinoic acid-inducible gene-I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) mediate responses to cytosolic dsDNA or dsRNA, respectively. TLR-induced responses are more robust than those induced by cytosolic DNA- or RNA- sensors, the later usually being limited to interferon regulatory factor 3 (IRF3)-dependent type I interferon (IFN) induction and nuclear factor (NF)-,B activation. Interestingly, AIM2 is not capable of inducing type I IFN, but rather plays a role in caspase I activation. DNA- or RNA-like synthetic inhibitory oligonucleotides (INH-ODN) have been developed that antagonize TLR-7- and/or TLR-9-induced activation in autoimmune B cells and in type I IFN-producing dendritic cells at low nanomolar concentrations. It is not known whether these INH-ODNs have any agonistic or antagonistic effects on cytosolic DNA or RNA sensors. While this remains to be determined in the future, in vivo studies have already shown their potential for preventing spontaneous lupus in various animal models of lupus. Several groups are exploring the possibility of translating these INH-ODNs into human therapeutics for treating SLE and bacterial DNA-induced sepsis. [source] Perspectives and opportunities for novel antiviral treatments targeting virus fitnessCLINICAL MICROBIOLOGY AND INFECTION, Issue 7 2008M. Clementi Abstract Increasing data indicate that reduction of virus fitness may be beneficial for the host in persistent human infections caused by RNA viruses, and that virus fitness can be targeted in clinical practice. Analysis of virus fitness determinants in rapidly evolving RNA viruses has revealed that virus extinction may be obtained in vitro by forcing virus populations through a lethal mutagenesis process, thus abolishing virus replication by violation of the error threshold. It will be important in the future to evaluate the use of novel compounds designed specifically to modulate virus fitness in vivo, and to optimise diagnostic virology methods to enable a reliable large-scale evaluation of this approach. [source] Sequence and structure relatedness of matrix protein of human respiratory syncytial virus with matrix proteins of other negative-sense RNA virusesCLINICAL MICROBIOLOGY AND INFECTION, Issue 10 2004K. Latiff Abstract Matrix proteins of viruses within the order Mononegavirales have similar functions and play important roles in virus assembly. Protein sequence alignment, phylogenetic tree derivation, hydropathy profiles and secondary structure prediction were performed on selected matrix protein sequences, using human respiratory syncytial virus matrix protein as the reference. No general conservation of primary, secondary or tertiary structure was found, except for a broad similarity in the hydropathy pattern correlating with the fact that all the proteins studied are membrane-associated. Interestingly, the matrix proteins of Ebola virus and human respiratory syncytial virus shared secondary structure homology. [source] | |||||||||||||||||||||||||