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Background: Synergy exists between DNA and RNA viruses. It was found that the Human Immunodeficiency Viruses (HIV-1) are RNA viruses at the origin of Acquired Immune Deficiency Syndrome (AIDS). The DNA recurrent herpes diseases are associated to AIDS virus at the origin of Sub-Saharan cancer AIDS pandemic. Objective: It is speculated that a varicella virus (HHV-3) immune defect could originate HSV- 1/HSV-2 recurrent herpes diseases that can be cured by varicella vaccine (2012). Methods: At a Symposium held in Kampala, Uganda (1962), impressive Sub-Saharan cancer epidemics: Hodgkin lymphomas and Kaposi sarcomas have been reported since the onset of the 20th century and remained unexplained. Over one thousand publications related to these cancer epidemics were presented. For millenniums, Bantu populations have been living in tropical forests close to chimpanzees infected by Simian Immune Deficiency viruses (SIV). SIV became Human Immune Deficiency viruses (HIV-1). AIDS is a zoonosis. Results: The DNA and RNA viruses, herpes with HIV-1 viruses, are correlated to Sub- Saharan AIDS infections. They induce an extensive immune deficiency with other herpes viruses such as HHV-4 and HHV-8, which are linked to lymphomas and Kaposi sarcomas. It is postulated that a primary HHV-3 immune weakness could be linked to herpes partnership with AIDS pandemic. Conclusion: The Oka, anti-HHV-3, varicella vaccine is able to cure HSV1/HSV2 recurrent herpes diseases. It induces a specific increase of the varicella antibodies. Thus varicella vaccination could prevent herpes recurrences in Sub-Saharan Africa. One- child dose varicella vaccine could be proposed as the first step to overcome HHV-3 herpes deficiency in order to prevent AIDS pandemic.

This work was supported in part through Battelle Memorial Institute?s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I (J.H.K.). This work was also funded in part by National Institutes of Health (NIH) contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (R.B.T.) Rega Institute. Infectious Diseases unit. Leuven, Leuven, Belgium. United States Department of Agriculture. Agricultural Research Service. US Horticultural Research Laboratory. Fort Pierce, FL, USA. Ministry of Health of the Russian Federation. N. F. Gamaleya Federal Research Center for Epidemiology and Microbiology. D. I. Ivanovsky Institute of Virology. Moscow, Russia. University of Ljubljana. Ljubljana Faculty of Medicine. Ljubljana, Slovenia. Mississippi State University. Department of Biological Sciences. Mississippi State, MS, USA. University of Texas Medical Branch. Galveston, TX, USA. Institute of Diagnostic Virology. Friedrich-Loefer-Institut. Greifswald-Insel Riems, Germany. Centers for Disease Control and Prevention. Division of High-Consequence Pathogens and Pathology. Viral Special Pathogens Branch. Atlanta, GA, USA. Colorado State University. Department of Microbiology. Immunology & Pathology, Arthropod-borne and Infectious Diseases Laboratory. Fort Collins, CO, USA. Columbia University. Center for Infection and Immunity. Department of Epidemiology, Mailman School of Public Health. New York, NY, USA. University of California. Department of Molecular Biology and Biochemistry. Irvine, CA, USA. National Health Laboratory Service. Division of Virology. Bloemfontein. Republic of South Africa / University of the Free State. Division of Virology. Bloemfontein, Republic of South Africa. Colorado State University. Department of Microbiology. Immunology & Pathology, Arthropod-borne and Infectious Diseases Laboratory. Fort Collins, CO, USA. Unit? des Virus Emergents (Aix-Marseille Univ?IRD 190? Inserm 1207?IHU M?diterran?e Infection). Marseille, France. International Rice Research Institute. Plant Breeding Genetics and Biotechnology Division. Los Ba?os, Philippines. Les MandinauxLe Grand Madieu. France. The Scripps Research Institute. Department of Immunology and Microbiology IMM-6. La Jolla, USA. Unit? des Virus Emergents (Aix-Marseille Univ?IRD 190?Inserm 1207?IHU M?diterran?e Infection). Marseille, France. University of California. Department of Medicine. San Francisco, USA / University of California. Department of Biochemistry and Biophysics. San Francisco, USA / University of California. Department of Microbiology. San Francisco, USA. Istituto Agronomico Mediterraneo di Bari. Valenzano, Italy. Public Health Agency of Canada. National Microbiology Laboratory. Zoonotic Diseases and Special Pathogens. Winnipeg, Canada. Mayo Clinic. Department of Molecular Medicine. Rochester, USA. Istituto Agronomico Mediterraneo di Bari. Valenzano, Italy. Hacettepe University. Faculty of Medicine. Department of Medical Microbiology. Virology Unit. Ankara, Turkey. University of Texas Medical Branch. Galveston, TX, USA. United States Army Medical Research Institute of Infectious Diseases. Fort Detrick, Frederick, USA. Chinese Center for Disease Control and Prevention. National Institute for Viral Disease Control and Prevention. Beijing, China. Kansas State University. Center of Excellence for Emerging and Zoonotic Animal Disease. Manhattan, USA. Chinese Center for Disease Control and Prevention. National Institute for Communicable Disease Control and Prevention. Beijing, China / Fudan University. Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences. Shanghai, China. WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research. Bernhard-Nocht Institute for Tropical Medicine. Department of Virology. Hamburg, Germany. CNRS- Paris-Diderot. Institut Jacques Monod. Paris, France. The University of Queensland. School of Chemistry and Molecular Biosciences. Australian Infectious Diseases Research Centre. Brisbane, Australia. Public Health England. Salisbury, UK. Centers for Disease Control and Prevention. Fort Collins, USA. Indian Agricultural Research Institute. Division of Plant Pathology. New Delhi, India. Seoul National University. College of Agriculture and Life Sciences. Department of Agricultural Biotechnology, Center for Fungal Pathogenesis. Seoul, Korea. Humboldt-University Berlin, and Berlin Institute of Health. corporate member of Free University Berlin. Institute of Virology. Charit?-Universit?tsmedizin Berlin. Berlin, Germany / German Centre for Infection Research. Berlin, Germany. Humboldt-University Berlin, and Berlin Institute of Health. corporate member of Free University Berlin. Institute of Virology. Charit?-Universit?tsmedizin Berlin. Berlin, Germany / Slovak Academy of Sciences. Biomedical Research Center. Bratislava, Slovakia. Karolinska University Hospital. Center for Infectious Medicine, Karolinska Institutet. Department of Medicine Huddinge. Stockholm, Sweden. Wageningen University. Department of Plant Sciences. Laboratory of Virology. Wageningen, The Netherlands. Centers for Disease Control and Prevention. Fort Collins, USA. University of Washington. Department of Microbiology. Washington, USA. University of Louisville. School of Medicine. The Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases. Department of Pharmacology and Toxicology. Louisville, USA. Humboldt-University Berlin, and Berlin Institute of Health. corporate member of Free University Berlin. Institute of Virology. Charit?-Universit?tsmedizin Berlin. Berlin, Germany / German Centre for Infection Research. Berlin, Germany. University of Bari Aldo Moro. Department of Plant, Soil and Food Sciences. Bari, Italy. University of Hamburg. Biocentre Klein Flottbek. Hamburg, Germany. Folkhalsomyndigheten. Stockholm, Sweden. University of Hamburg. Biocentre Klein Flottbek. Hamburg, Germany. Washington State University. Irrigated Agricultural Research and Extension Center. Department of Plant Pathology. Prosser, USA. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Centro de Inova??es Tecnol?gicas. Ananindeua, PA, Brasil. United States Army Medical Research Institute of Infectious Diseases. Fort Detrick, Frederick, USA. Aristotle University of Thessaloniki. National Reference Centre for Arboviruses and Haemorrhagic Fever Viruses. Department of Microbiology, Medical School. Thessaloniki, Greece. National Health Laboratory Service. National Institute for Communicable Diseases. Centre for Emerging Zoonotic and Parasitic Diseases. Sandringham, South Africa / University of Pretoria. Centre for Viral Zoonoses, Faculty of Health Sciences. Department of Medical Virology. Pretoria South Africa. University of Texas Medical Branch. Galveston, TX, USA. University of Helsinki. Department of Virology. Medicum, Helsinki, Finland. United States Army Medical Research Institute of Infectious Diseases. Fort Detrick, Frederick, USA. Universidade de Bras?lia. Departamento de Biologia Celular. Bras?lia , DF, Brazil. Universidad Nacional de La Plata - Consejo Nacional de Investigaciones Cient?ficas y T?cnicas. Centro Cientifico Technol?gico-La Plata. Instituto de Biotecnolog?a y Biolog?a Molecular. La Plata, Argentina. Institut Pasteur de Dakar. Dakar, Senegal. University of Maryland School of Medicine. Institute of Human Virology. Baltimore, USA. National Agriculture and Food Research Organization. Department of Planning and Coordination. Tsukuba, Japan. United States Army Medical Research Institute of Infectious Diseases. Fort Detrick, Frederick, USA. MRC-University of Glasgow Centre for Virus Research. Glasgow, UK. University of Tokyo. Asian Center for Bioresources and Environmental Sciences. Tokyo, Japan. University of Oxford. Department of Medicine. Oxford, UK. Bioinformatics Scientific Institute IRCCS E. MEDEA. Bosisio Parini, Italy. Korea University. College of Medicine. Department of Microbiology. Seoul. Republic of Korea. Centers for Disease Control and Prevention. Division of High-Consequence Pathogens and Pathology. Viral Special Pathogens Branch. Atlanta, GA, USA. Colorado State University. Immunology and Pathology. Department of Microbiology. Fort Collins, USA. University of Texas Medical Branch. Galveston, TX, USA. CNR. Institute for Sustainable Plant Protection. Torino, Italy. Fujian Agriculture and Forestry University. Institute of Plant Virology. Fujian Province Key Laboratory of Plant Virology. Fuzhou, China. North Carolina State University. Department of Entomology and Plant Pathology. Raleigh, USA. National Chung Hsing University. Department of Plant Pathology. Taichung, Taiwan. Universidade Federal de Vi?osa. Departamento de Fitopatologia/BIOAGRO. Vi?osa, MG, Brazil. Chinese Center for Disease Control and Prevention. National Institute for Communicable Disease Control and Prevention. Beijing, China / Fudan University. Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences. Shanghai, China. Chinese Academy of Agricultural Sciences. Institute of Plant Protection. State Key Laboratory for Biology of Plant Diseases and Insect Pests. Beijing, China. National Institutes of Health (NIH). National Institute of Allergy and Infectious Diseases (NIAID). Division of Clinical Research (DCR). Integrated Research Facility at Fort Detrick (IRF-Frederick). Frederick, USA. In October 2018, the order Bunyavirales was amended by inclusion of the family Arenaviridae, abolishment of three families, creation of three new families, 19 new genera, and 14 new species, and renaming of three genera and 22 species. This article presents the updated taxonomy of the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

International audience; In 2012, a 50 year-old athletic male presented with weakness, pain and unilateral phrenic paralysis, followed by bilateral phrenic paralysis with deep dyspnea. In 2013, the Parsonage-Turner syndrome was diagnosed. When the patient was seen in September 2014 for the first time, he was facing phrenic neuromuscular failure, which led to the hypothesis of neurotropic herpes viruses. A control of the global serological anti-Herpes immunity to analyze his antibody (Ab) levels confirmed herpes immune genetic deficiency. An appropriate herpes chemotherapy treatment was proposed. Immediately, a spectacular recovery of the patient was observed, and after a few weeks, the respiratory function tests showed normal values. The hypothesis of the inductive role of viruses of the herpes family in the Parsonage-Turner syndrome was thus substantiated. The patient's immune deficiency covers the HSV2, HHV3, HHV4, HHV5 and HHV6 Ab levels. This led to the control of herpes in the family lineage: indeed, his daughter presented alterations of her serological herpes Ab levels.

Top-levelled international football and rugby teams usually train in teams on other sports such as volleyball or handball. Sportsmen work on their flexibility, their quickness, and the group cohesion. The problem of the top-levelled sports teams consist in training altogether: quickness, efficiency, and coordination exercises in other special fields.

The RNA genome of turnip yellow mosaic virus (TYMV) consists of more than 6,000 nucleotides. During a study of the roles of the two hairpins located in its 90-nucleotide 5′ untranslated region, it was observed that stabilization of the 5′-proximal hairpin leads to a delay in the development of symptoms on plants. This delay in symptom development for both locally and systemically infected leaves was found to be dependent on a change in the free energy of the hairpin caused by introduced mutations. A protoplast transfection assay revealed that the accumulation of plus-strand full-length RNA and subgenomic RNA, as well as protein expression levels, was affected by hairpin stability. Stabilization of this hairpin inhibited translation. A model is proposed in which a destabilized 5′-proximal hairpin allows maximal translation of the viral proteins. It is suggested that this hairpin may exist in close proximity to the 5′ cap as long as its stability is low enough to enable translation. However, at an acidic pH, the hairpin structure becomes more stable and is functionally transformed into the initiation signal for viral packaging. Slightly acidic conditions can be found in chloroplasts, where TYMV assembly is driven by a low pH generated by active photosynthesis.

Among the negative RNA viruses, ambisense RNA viruses or 'ambisense viruses' occupy a distinct niche. Ambisense viruses contain at least one ambisense RNA segment, i.e. an RNA that is in part of positive and in part of negative polarity. Because of this unique gene organization, one might expect ambisense RNA viruses to borrow expression strategies from both positive and negative RNA viruses. However, they have little in common with positive RNA viruses, but possess many features of negative RNA viruses. Transcription and/or replication of their RNAs appear generally to be coupled to translation. Such coupling might be important to ensure temporal control of gene expression, allowing the two genes of an ambisense RNA segment to be differently regulated. Ambisense viruses can infect one host asymptomatically and in certain cases, they can lethally infect two hosts of a different kingdom. A possible model to explain the differential behavior of a given virus in different hosts could be that perturbation of the translation machinery would lead to differences in the severity of symptoms.

Most plant viruses rely on the production of subgenomic RNAs (sgRNAs) for the expression of their genes and survival in the plant. Although this is a widely adopted strategy among viruses, the mechanism(s) whereby sgRNA production occurs remains poorly defined. Turnip yellow mosaic tymovirus (TYMV) is a positive-stranded RNA virus that produces an sgRNA for the expression of its coat protein. Here we report that the subgenomic promoter sequence of TYMV is located on a 494-nucleotide fragment, containing previously identified highly conserved sequence elements, which are shown here to be essential for promoter function. After duplication, the subgenomic promoter can be inserted into the coat protein open reading frame, giving rise to the in vivo production of a second sgRNA. It is suggested that this promoter can function when contained on a different molecule than viral genomic RNA. This interesting trait may be of general use for plant and plant virus research.

An improved method for preparation of protoplasts of Arabidopsis thaliana cells grown in suspension culture is presented. This method is fast, reliable and can be used for the production of virtually an unlimited number of protoplasts at any time. These protoplasts can be transformed efficiently with RNA from turnip yellow mosaic tymovirus (TYMV) by polyethyleneglycol-mediated transfection. The simple transfection procedure has been optimized at various steps. Replication of TYMV can be monitored routinely by detection of the coat protein in as few as 2×10 4 infected protoplasts.

The Potyvirus helper component-proteinase (HC-Pro) binds nonspecifically to single-stranded nucleic acids with a preference for RNA. To delineate the regions of the protein responsible for RNA binding, deletions were introduced into the full-length Potato potyvirus Y HC-Pro gene carried by an Escherichia coli expression vector. The corresponding proteins were expressed as fusions with the maltose-binding protein, purified, and assayed for their RNA-binding capacity. The results obtained by UV cross-linking and Northwestern blot assays demonstrated that the N- and C-terminal regions of HC-Pro are dispensable for RNA binding. They also revealed the presence of two independent RNA-binding domains (designated A and B) located in the central part of HC-Pro. Domain B appears to contain a ribonucleoprotein (RNP) motif typical of a large family of RNA-binding proteins involved in several cellular processes. The possibility that domain B consists of an RNP domain is discussed and suggests that HC-Pro could constitute the first example of a plant viral protein belonging to the RNP-containing family of proteins.

The first ∼60 amino acids of the N-terminal part of the potyvirus helper component-proteinase (HC-Pro) include highly conserved residues comprising a Cys-rich region. In the present study, the domain in Potato virus Y sufficient for self-interaction was mapped using the yeast two-hybrid system to the 83 N-terminal amino acids of HC-Pro. Mutations in the conserved His and two Cys residues within the Cys-rich region have a strong debilitating effect on self-interaction when introduced in the full-length HC-Pro, but not when introduced in the N-terminal fragment.

Given the small size of their genome, the genetic information of viruses is extremely compact, and non-coding regions are very limited as compared to those of prokaryotic and eukaryotic cell systems. Viruses utilize cell components at all levels of the replication cycle for their own benefit, not the least being the translation machinery. They have also evolved a number of highly sophisticated strategies to produce and regulate the production of the proteins required for their propagation. In addition, these proteins are often multifunctional, encoding several essential virus-specific proteins. At the level of transcription, these strategies include splicing, the production of subgenomic RNAs from virus templates and cap-snatching. At the level of translation, regulation exists at all steps: initiation, elongation and termination. Furthermore, viruses frequently resort to co- and/or post-translational cleavage of a polyprotein precursor to yield the mature proteins.

Using the yeast two-hybrid system, a screen was performed for possible interactions between the proteins encoded by the 5′ region of potyviral genomes [P1, helper component-proteinase (HC-Pro), and P3]. A positive self-interaction involving HC-Pro was detected with lettuce mosaic virus (LMV) and potato virus Y (PVY). The possibility of heterologous interaction between the HC-Pro of LMV and of PVY was also demonstrated. No interaction involving either the P1 or the P3 proteins was detected. A series of ordered deletions from either the N- or C-terminal end of the LMV HC-Pro was used to map the domain involved in interaction to the 72 N-terminal amino acids of the protein, a region known to be dispensable for virus viability but necessary for aphid transmission. A similar but less detailed analysis mapped the interacting domain to the N-terminal half of the PVY HC-Pro.

Because of the small size of their genome, viral genes have been forerunners in helping us understand gene expression. It is also because of their small size that viruses have elaborated the amazing variety of strategies that enables them to produce all the proteins they require for their multiplication. As a consequence, many of the strategies of expression known to occur in cell systems were first demonstrated in viruses. The aim of this review is to highlight the contribution of viruses to our knowledge of cell processes.

The role of the 3' noncoding (NC) region of Physalis mottle tymovirus genomic RNA in the multiplication of the virus was examined using an in vivo protoplast assay system. Coat protein (CP) synthesis was specifically inhibited by sense 3' NC region transcripts. To establish the role of the pseudoknot structure present in the NC region in virus multiplication, four site-specific mutants, two of which disrupted the pseudoknot structure while the other two restored the structure, were constructed. Interestingly, none of the four sense mutant transcripts inhibited CP synthesis, suggesting that the specific sequence representing the 3' terminal pseudoknot structure may play an important role in virus multiplication. However, the wild-type antisense 3' NC transcript as well as the four antisense mutant transcripts inhibited CP synthesis, suggesting that the inhibitions by antisense transcripts could be due to the formation of RNA-RNA hybrids at the 3' end of the genomic RNA.

The first demonstration on the aminoacylation capacity of the RNA genome of a plant virus appeared more than 25 years ago. Shortly thereafter, aminoacylation of the RNA genome of a number of other plant viruses was observed. This led to considerable work on the tRNA-like region of these viral RNAs, and to the first demonstration of the presence of pseudoknots in their folding pattern. In spite of the vast amount of efforts put into trying to understand the reason for the aminoacylation capacity of certain viral RNA genomes, as yet no clear general conclusion emerges. It rather looks as though the reason for aminoacylation may be different for different viruses, and that aminoacylation may operate at different levels in the virus life cycle. Given that certain RNA viruses possess structures which resemble that of tRNAs at their 5'- or 3'-termini, it is most likely that convergent evolution may have dominated the appearance of such structures in the virus world.

Introduction. Most plant viruses contain an RNA genome and are traditionally classified into genera (or families) of which there are over 40. This large number reflects the formidable variety that exists among plant RNA viruses. The genomes are mostly single-stranded (ss) and of positive polarity; in a few genera, they are negative sense, ambisense, or double-stranded (ds). The different strategies used by viruses for their amplification have been described at length. However, it is often difficult to find in a summarized form the main data on genome features of all groups of plant RNA viruses. The last review article along these lines (Davies & Hull, 1982) dates from before any full-length RNA sequence of a plant RNA virus was published; never-theless, a few books have more recently included this subject (Francki et al., 1991; Matthews, 1991).

Recently, cDNA clones encoding the bovine (b) [M. Garret, B. Pajot, V. Trezeguet, J. Labouesse, M. Merle, J.-C. Gandar, J.-C. Gandar, J.-P. Benedetto, M.-L. Sallafranque, J. Alterio, M. Gueguen, C. Sarger, B. Labouesses and J. Bonnet (1991) Biochemistry 30, 7809–7817] and human (h) [L. Yu. Frolova, M. A. Sudomoina, A. Yu. Grigorieva, O. L. Zinovieva and L. L. Kisselev (1991) Gene 109, 291–296] tryptophanyl-tRNA synthetases (TrpRS) were sequnced; the deduced amino acid sequences exhibit typical structural features of class I aminoacyl-tRNA synthetases [G. Eriani, M. Delarue, O. Poch, J. Gangloff and D. Moras (1990) Nature 237, 203–206] and limited, although significant, similarity with bacterial TrpRS. Independently, it was shown that a major protein whose synthesis is stimulated in human cell cultures by interferon γ [J. Fleckner, H. H. Rasmussen and J. Justesen (1991) Proc. Natl Acad. Sci. USA 88, 11 520–11 524], and interferons γ or α [B. Y. Rubin, S. L. Anderson, L. Xing, R. J. Powell and W. P. Tate (1991) J. Biol. Chem. 226, 24 245–24 248], exhibits TrpRS activity and an amino acid sequence identical to that of hTrpRS. The amino acid sequences of bTrpRS and hTrpRS are highly similar and are surprisingly very similar to the amino acid sequence deduced from a cloned and sequenced cDNA reported to encode rabbit (r) peptide-chain-release factor (RF) [C. C. Lee, W. J. Craigen, D. M. Muzny, E. Harlow and C. T. Caskey (1990) Proc. Natl Acad. Sci. USA 87, 3508–3512]. This close similarity between mammalian TrpRS and cloned RF is unexpected given the distinct functional properties of these proteins. Consequently, the question arises as to whether the mammalian TrpRS and RF activities reside on identical or very similar polypeptides. Alternatively, one may assume that the cloned rabbit cDNA encodes a protein other than rRF. Several properties (immunochemical, biochemical and physico-chemical) of mammalian TrpRS and RF have been compared. rTrpRS and rRF have distinct thermostabiliy behaviours, and dissimilar chromatographic profiles on phosphocellulose. Both the anti-bTrpRS polyclonal antibodies and the monoclonal antibody Am2 strongly inhibit the bTrpRS and hTrpRS aminoacylation activities, but not the rRF activity. In addition, neither bTrpRS nor hTrpRS exhibit RF activity. It is concluded that (a) the functional centers responsible for the TrpRS and RF activities are structurally and functionally dissimilar and could hardly belong to the same protein domain; (b) RF and TrpRS probably reside on different polypeptide chains encoded by different genes, although it is still not excluded that the RF- and TrpRS-specific domains are situated on one and the same polypeptide chain; (c) the rabbit cDNA believed to encode RF, presumably encodes rTrpRS; this would explain why its deduced amino acid sequence has no similarity with bacterial RFs but is very similar to mammalian TrpRS.

The development of techniques based on fluorescence has made it possible to create new types of assays that represent an advantageous alternative to old tests relying on radioactivity. Such a novel approach has been applied to develop a high-throughput assay to measure the helicase activity of the hepatitis C virus (HCV) NS3 protein and the inhibitory potential of several classes of compounds. The NS3 helicase is one of the most promising targets of anti-HCV-oriented screening of compounds due to the urgent need for more effective and tolerable drugs. The 96- or 384-well microplate assay that we developed is based on the use of a quenched double-stranded DNA substrate labeled with a fluorophore (Cy3 or FAM) and with a Black Hole Quencher 1 or 2. It allows for direct (real-time) measurements of substrate unwinding and inhibition of unwinding by anti-helicase compounds. After a few modifications of buffers and assay conditions this method can be applied to various variants of HCV helicase and other proteins with helicase activities.

Dengue is the most important cause of mosquito-borne virus diseases in tropical and subtropical regions in the world. Severe clinical outcomes such as dengue hemorrhagic fever and dengue shock syndrome are potentially fatal. The epidemiology of dengue has undergone profound changes in recent years, due to several factors such as expansion of the geographical distribution of the insect vector, increase in traveling, and demographic pressure. As a consequence, the incidence of dengue has increased dramatically. Since mosquito control has not been successful and since no vaccine or antiviral treatment is available, new approaches to this problem are needed. Consequently, an in-depth understanding of the molecular and cellular biology of the virus should be helpful to design efficient strategies for the control of dengue. Here, we review the recently acquired knowledge on the molecular and cell biology of the dengue virus life cycle based on newly developed molecular biology technologies.

No information exists on the organization and mechanisms of expression of the genome of rice hoja blanca virus (RHBV), a member of the tenuivirus group, but here we describe the first steps in its characterization. RHBV contains four ssRNA and three dsRNA species, the sizes of which were estimated by native and denaturing gel electrophoresis. Hybridization analyses using 32P-labelled riboprobes of viral and viral complementary polarities showed that unequal amounts of the two polarities of at least the smallest RNA are present in the virion, and indicated that the dsRNA species contain the same information as the ssRNA species of corresponding size. Total RHBV RNA directs the synthesis of two major proteins of 23K and 21K in vitro. RNA3 directs the synthesis of a 23K protein designated NS3, and RNA4 of a 21K protein designated NS4. The NS4 protein corresponds to the non-structural protein that accumulates in RHBV-infected rice tissue. The nuclecocapsid protein is not translated from either total RHBV RNA or any individual RHBV RNA in vitro.

The development of techniques based on fluorescence has made it possible to create new types of assays that represent an advantageous alternative to old tests relying on radioactivity. Such a novel approach has been applied to develop a high-throughput assay to measure the helicase activity of the hepatitis C virus (HCV) NS3 protein and the inhibitory potential of several classes of compounds. The NS3 helicase is one of the most promising targets of anti-HCV-oriented screening of compounds due to the urgent need for more effective and tolerable drugs. The 96- or 384-well microplate assay that we developed is based on the use of a quenched double-stranded DNA substrate labeled with a fluorophore (Cy3 or FAM) and with a Black Hole Quencher 1 or 2. It allows for direct (real-time) measurements of substrate unwinding and inhibition of unwinding by anti-helicase compounds. After a few modifications of buffers and assay conditions this method can be applied to various variants of HCV helicase and other proteins with helicase activities.

Publisher Summary Virus‐like particles (VLPs), formed by the structural elements of viruses, have received considerable attention over the past two decades. The number of reports on newly obtained VLPs has grown proportionally with the systems developed for the expression of these particles. The chapter outlines the recent achievements in two important fields of research brought about by the availability of VLPs produced in a foreign host. These are: (1) The requirements for VLP assembly and (2) the use of VLPs as carriers for foreign epitopes. VLP technology is a rapidly advancing domain of molecular and structural biology. Extensive progress in VLP studies was achieved as the insect cell based protein production system was developed. This baculovirus expression system has many advantages for the synthesis of viral structural proteins resulting in the formation of VLPs. It allows production of large amounts of correctly folded proteins while also providing cell membranes that can serve as structural elements for enveloped viruses. These features give us the opportunity to gain insights into the interactions and requirements accompanying VLP formation that are similar to the assembly events occurring in mammalian cells. Other encouraging elements are the ability to easily scale up the system and the simplicity of purification of the assembled VLPs. The growing number of VLPs carrying foreign protein fragments on their surface and studies on the successful assembly of these chimeric molecules is a promising avenue towards the development of a new technology, in which the newly designed VLPs will be directed to particular mammalian cell types by exposing specific binding domains. The progress made in modeling the surface of VLPs makes them to date the best candidates for the design of delivery systems that can efficiently reach their targets.

Virus‐like particles (VLPs), formed by the structural elements of viruses, have received considerable attention over the past two decades. The number of reports on newly obtained VLPs has grown proportionally with the systems developed for the expression of these particles. The chapter outlines the recent achievements in two important fields of research brought about by the availability of VLPs produced in a foreign host. These are: (1) The requirements for VLP assembly and (2) the use of VLPs as carriers for foreign epitopes. VLP technology is a rapidly advancing domain of molecular and structural biology. Extensive progress in VLP studies was achieved as the insect cell based protein production system was developed. This baculovirus expression system has many advantages for the synthesis of viral structural proteins resulting in the formation of VLPs. It allows production of large amounts of correctly folded proteins while also providing cell membranes that can serve as structural elements for enveloped viruses. These features give us the opportunity to gain insights into the interactions and requirements accompanying VLP formation that are similar to the assembly events occurring in mammalian cells. Other encouraging elements are the ability to easily scale up the system and the simplicity of purification of the assembled VLPs. The growing number of VLPs carrying foreign protein fragments on their surface and studies on the successful assembly of these chimeric molecules is a promising avenue towards the development of a new technology, in which the newly designed VLPs will be directed to particular mammalian cell types by exposing specific binding domains. The progress made in modeling the surface of VLPs makes them to date the best candidates for the design of delivery systems that can efficiently reach their targets.

Publisher Summary This chapter provides an updated view of the host factors that are, at present, believed to participate in replication/transcription of RNA viruses. One of the major hurdles faced when attempting to identify host factors specifically involved in viral RNA replication/transcription is how to discriminate these factors from those involved in translation. Several of the host factors shown to affect viral RNA synthesis are factors known to be involved in protein synthesis, for example, translation factors. In addition, some of the factors identified to date appear to influence viral RNA amplification as well as viral protein synthesis, and translation and replication are frequently tightly associated. Several specific host factors actively participating in viral RNA transcription/replication have been identified and the regions of host protein/replicase or host protein/viral RNA interaction have been determined. The chapter centers exclusively on those factors that appear functionally important for viral amplification. It presents a list of the viruses for which a specific host factor associates with the polymerase, affecting viral genome amplification. It also indicates the usually accepted cell function of the factor and the viral polymerase or polymerase subunit to which the host factor binds.

Publisher Summary This chapter discusses the nature and function of eukaryotic viral genome-linked proteins (VPgs) and outlines some of the remarkable features of these proteins. The first indications that a viral protein could form a stable complex with the genome of eukaryotic viruses were based on electron microscopy analyses and various biochemical techniques and were obtained with Adenoviridae. In RNA viruses, the term viral genome-linked protein was coined for the poliovirus protein and has been adopted for virtually all the proteins linked to RNA viruses. For the sake of simplification and to facilitate comprehension, the RNA and the DNA viruses whose genome possesses a covalently bound protein have been treated separately. In positive single-stranded RNA viruses, the VPg is always synthesized as part of a larger polyprotein from which it is excised by a viral proteinase that is also part of the polyprotein. The genomes of certain phages and viruses have long been known to covalently bind a viral protein. This feature was subsequently shown to occur also in cell systems. It is thus not an exclusive property of viruses. Indeed, extensive work on cellular topoisomerases, and the tumor suppressor p53 has demonstrated that these proteins can be covalently bound to a nucleic acid.

Using selection-amplification, we have isolated RNAs with affinity for translation termination factors eRF1 and eRF1•eRF3 complex. Individual RNAs not only bind, but inhibit eRF1-mediated release of a model nascent chain from eukaryotic ribosomes. There is also significant but weaker inhibition of eRF1-stimulated eRF3 GTPase and eRF3 stimulation of eRF1 release activity. These latter selected RNAs therefore hinder eRF1•eRF3 interactions. Finally, four RNA inhibitors of release suppress a UAG stop codon in mammalian extracts dependent for termination on eRF1 from several metazoan species. These RNAs are therefore new specific inhibitors for the analysis of eukaryotic termination, and potentially a new class of omnipotent termination suppressors with possible therapeutic significance.

The vast majority of plant virus groups contain an RNA genome, most frequently of positive polarity. This chapter provides an updated overview of genome of such plant viruses stressing the functions of coding and non coding regions of genome in virus amplification. Three concise tables accompany the text. In each table, the viruses are presented in alphabetical order by genera as officially recognized in the Plant Virus Classification of the International Committee on Taxonomy of Viruses (1996). Table 1 presents general features of RNA genomes and their associated RNAs like satellite RNA (sat-RNA) and defective interfering RNA (DI). Table 2 shows further major characteristics of viruses with a single-strand RNA (ssRNA) genome. Table 3 classifies the viruses in supergroups where these have been established, outlines gene arrangements (also consult chapter 3), and gives the main translation strategies (chapter 4) used by plant RNA viruses. Recent key references as well as certain other references, not mentioned in the review by Zaccomer et al. (1995), are provided. A few virus groups are not presented, due to lack of sufficient sequence data concerning them. These are the fabaviruses, betacryptoviruses and cytorhabdoviruses. Virus-related RNA molecules (DI and sat-RNA) and viroids are not discussed here.

It is known from experiments with bacteria and eukaryotic viruses that readthrough of termination codons located within the open reading frame (ORF) of mRNAs depends on the availability of suppressor tRNA(s) and the efficiency of termination in cells. Consequently, the yield of readthrough products can be used as a measure of the activity of polypeptide chain release factor(s) (RF), key components of the translation termination machinery. Readthrough of the UAG codon located at the end of the ORF encoding the coat protein of beet necrotic yellow vein furovirus is required for virus replication. Constructs harbouring this suppressible UAG codon and derivatives containing a UGA or UAA codon in place of the UAG codon have been used in translation experiments in vitro in the absence or presence of human suppressor tRNAs. Readthrough can be virtually abolished by addition of bacterially-expressed eukaryotic RF1 (eRF1). Thus, eRF1 is functional towards all three termination codons located in a natural mRNA and efficiently competes in vitro with endogenous and exogenous suppressor tRNA(s) at the ribosomal A site. These results are consistent with a crucial role of eRF1 in translation termination and forms the essence of an in vitro assay for RF activity based on the abolishment of readthrough by eRF1.

This review is centered on the major strategies used by plant RNA viruses to produce the proteins required for virus multiplication. The strategies at the level of transcription presented here are synthesis of mRNA or subgenomic RNAs from viral RNA templates, and 'cap-snatching'. At the level of translation, several strategies have been evolved by viruses at the steps of initiation, elongation and termination. At the initiation step, the classical scanning mode is the most frequent strategy employed by viruses; however in a vast number of cases, leaky scanning of the initiation complex allows expression of more than one protein from the same RNA sequence. During elongation, frameshift allows the formation of two proteins differing in their carboxy terminus. At the termination step, suppression of termination produces a protein with an elongated carboxy terminus. The last strategy that will be described is co- and/or post-translational cleavage of a polyprotein precursor by virally encoded proteinases. Most (+)-stranded RNA viruses utilize a combination of various strategies.

Introduction. The genus Potyvirus, family Potyviridae, is the largest genus of plant viruses with 180 members or possible members (Brunt, 1992). Potyviruses are flexuous filamentous particles which contain a single-stranded RNA genome of positive polarity possessing a covalently linked 5′-terminal viral protein (VPg) and a 3′-terminal poly(A) tail (reviewed in Riechmann et al., 1992). They are transmitted from plant to plant by aphids in a non-persistent manner, and this process is dependent on the presence of two virus-encoded proteins (reviewed in Pirone, 1991). One of these, the helper component-proteinase (HC-Pro) has attracted renewed attention during the last few years due to its multifunctionality and to it being implicated in different steps of the potyvirus life cycle. The properties, as well as the established and postulated functions of this protein, are reviewed.

The large non-structural polyprotein (206 kDa) of turnip yellow mosaic tymovirus (TYMV) undergoes auto-cleavage, producing N- and C-terminal proteins. Here we show that the viral proteinase responsible for this event is active when produced in Escherichia coli, as monitored in Western blots by examining the generation of the C-terminal cleavage product after induction by IPTG. The outer boundaries and critical amino acids of the proteinase domain were characterized by deletion analysis and site-directed mutagenesis. A miniproteinase of 273 residues resulting from combined N- and C- terminal deletions still performed efficient cleavage. Sequence analysis of the bacterially-purified C-terminal cleavage product indicated that cleavage occurs between Ala1259 and Thr1260 of the non-structural protein.

THE termination of protein synthesis in ribosomes is governed by termination (stop) codons in messenger RNAs and by polypeptide chain release factors (RFs). Although the primary structure of prokaryotic RFs and yeast mitochrondrial RF is established1–4, that of the only known eukaryotic RF (eRF)5 remains obscure. Here we report the assignment of a family of tightly related proteins (designated eRFl) from lower and higher eukaryotes which are structurally and functionally similar to rabbit eRF. Two of these proteins, one from human6 and the other from Xenopus laevis7 , have been expressed in yeast and Escherichia coli, respectively, purified and shown to be active in the in vitro RF assay. The other protein of this family, sup45 (supl) of Saccharomyces cerevisiae, is involved in omnipotent suppression during translation8–12. The amino-acid sequence of the eRFl family is highly conserved. We conclude that the eRFl proteins are directly implicated in the termination of translation in eukaryotes.

Introduction. The tenuiviruses are a most unusual type of virus about which little was known until recently. They were officially recognized as a plant virus group in 1983 (reviewed in Gingery, 1988). They are described in the Fifth Report of the International Committee on Taxonomy of Viruses as non-enveloped plant viruses, with possibly a negative ssRNA genome (Francki et al., 1991). Five viruses belong to this group, the type member rice stripe virus (RSV) first discovered in Japan in the 1890s, followed by maize stripe virus (MStV) in Mauritius in 1929, rice hoja blanca virus (RHBV) in Colombia in 1935, European wheat striate mosaic virus (EWSMV) in England in 1956, and rice grassy stunt virus (RGSV) in the Philippines in 1963 (reviewed in Gingery, 1988). Epidemics of RSV and RHBV cause important yield losses in rice-growing areas of Asia and the former U.S.S.R. (Toriyama, 1983), and of tropical America (Morales & Niessen, 1985) respectively.

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In order to evaluate new possibilities for protecting plants against virus infection by interference with viral replication, two chimeric genes were constructed in which the (+) strand 3′-terminal 100 nucleotides (nt) of the noncoding region of the turnip yellow mosaic virus (TYMV) genome were placed downstream from the sense or antisense cat coding region. The two chimeric genes were then introduced into the genome of rapeseed ( Brassica napus ) using an Agrobacterium rhizogenes vector system. Plants expressing high levels of either chimeric gene showed partial protection against infection by TYMV RNA or virions. One interesting feature of the protection is that a proportion of the inoculated transgenic plants does not become infected. Protection was overcome when the inoculum concentration was increased. RNA complementary to the initial transcript was detected after infection.

The complete sequence of rice hoja blanca virus (RHBV) RNA4 has been determined, based on the sequence of the corresponding cDNA clones. RNA4 consists of 1991 nucleotides with two open reading frames (ORFs). One putative ORF is located in the 5'-proximal region of the viral RNA4; it encodes a protein of predicted M(r) 20076 which corresponds to the major non-structural protein that accumulates in RHBV-infected rice plants, and which bears limited sequence identity with the helper component of tobacco vein mottling potyvirus. The other ORF is located in the 5'-proximal region of the viral complementary RNA4 and encodes a protein of predicted M(r) 32,469. Between the two ORFs is an intergenic region of 524 nucleotides, part of which can theoretically adopt a stable stem-loop structure; the 5' and 3' ends can potentially base-pair over 16 nucleotides, producing a pan-handle configuration. These characteristics are in favour of an ambisense coding strategy for RHBV RNA4.

We have previously shown that the Dictyostelium discoideum ribosomal protein L19 specifically binds Ca2+/calmodulin [Sonneman et al. (1991) J. Biol. Chem. 266, 23091-23096]. To investigate the role of calmodulin in the regulation of protein synthesis, we have now established an in vitro protein synthesizing system from Dictyostelium cells which can elongate polypeptide chains with high efficiency. Various calmodulin antagonists affected translation in this system. The inhibitory effects of the antagonists could be partially reversed by addition of calmodulin. A monoclonal antibody against D. discoideum calmodulin also specifically inhibited protein synthesis. Similar effects of calmodulin antagonists were found in a standard wheat germ in vitro translation system.

Mammalian aminoacyl-tRNA synthetases are indispensible components of the cell's protein-synthesizing machinery. Surprisingly, recent experiments have demonstrated that synthesis of tryptophanyl-tRNA synthetase (WRS) is markedly enhanced after incubation of human cells with interferons. Why is this housekeeping enzyme interferon-inducible? Several hypotheses have been suggested. One hypothesis, that premature termination of protein synthesis was involved, was boosted by the discovery that the deduced amino acid sequence of the mammalian peptide chain release factor (RF) closely resembled that of WRS. Further investigation, however, suggests that the DNA encoding RF was wrongly identified and in fact encodes a rabbit WRS subunit. Other hypotheses on the interferon-inducibility of WRS, including the possibility that the protein performs other, regulatory functions in addition to its core enzymic activity, remain to be explored.

Turnip yellow mosaic virus (TYMV) is the type-member of the tymovirus group which belongs to the Sindbis-like virus supergroup of (+)RNA viruses. TYMV infects members of the Cruciferae family. The genomic RNA directs the synthesis of two nonstructural overlapping proteins. It has recently been demonstrated that the larger one of 206K undergoes autocleavage yielding at least two products of 150K and 78K respectively, in vitro (1). The Smaller one of 69K is probably the movement protein (2).

Total nucleotide sequencing of the RNA genome of various tymoviruses has demonstrated that the overall genome organization of these viruses is identical. Furthermore, the strategies of expression of the turnip yellow mosaic virus (TYMV) genome have been established by in vitro translation studies; these include the synthesis of a subgenomic RNA, the utilization of overlapping open reading frames (ORFs) and maturation of a polyprotein. In the experiments described here, the strategies of expression of other tymovirus (eggplant mosaic virus, ononis yellow mosaic virus, belladonna mottle virus and physalis mottle virus) genomes have been compared to those used by the TYMV genome, in particular to determine whether these tymoviruses also resort to the expression of overlapping ORFs and maturation of a polyprotein.

Publisher Summary This chapter discusses the current knowledge of viral RNA replication. It presents both in vivo and in vitro data. The discussion in the chapter is restricted to those viruses for which RdRp complex has been isolated, irrespective of whether the enzyme requires exogenous RNA for its activity, and thus initiates and elongates complementary RNA chains, or whether it still retains RNA molecules (whose synthesis was initiated in vivo), and thus only elongates these RNA chains. RNA replication of viruses with a tripartite RNA genome, such as brome mosaic virus (BMV), cowpea chlorotic mottle virus (CCMV), cucumber mosaic virus (CMV), and alfalfa mosaic virus (AlMV), is described in the chapter, followed by the replication of viruses with a monopartite genome. These include turnip yellow mosaic virus (TYMV) and tobacco mosaic virus (TMV), then cowpea mosaic virus (CPMV) with a bipartite genome. RNA replication of velvet tobacco mottle virus (VTMoV) is last because of the limited information available on the replication mechanism of its RNA. The enzymes isolated from the first five viruses presented (BMV, CCMV, CMV, AIMV, and TYMV) are capable not only of elongating but also of initiating (–)–RNA strand synthesis because they are devoid of endogenous RNA; the RdRp's of the last three viruses (TMV, CPMV, and VTMoV) are only capable of elongating chains whose synthesis has been initiated in vivo .