Functional Long-Range RNA–RNA Interactions in Positive-Strand RNA Viruses
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Vector Capability of Xiphinema Americanum Sensu Lato in California 1
Journal of Nematology 21(4):517-523. 1989. © The Society of Nematologists 1989. Vector Capability of Xiphinema americanum sensu lato in California 1 JOHN A. GRIESBACH 2 AND ARMAND R. MAGGENTI s Abstract: Seven field populations of Xiphineraa americanum sensu lato from California's major agronomic areas were tested for their ability to transmit two nepoviruses, including the prune brownline, peach yellow bud, and grapevine yellow vein strains of" tomato ringspot virus and the bud blight strain of tobacco ringspot virus. Two field populations transmitted all isolates, one population transmitted all tomato ringspot virus isolates but failed to transmit bud blight strain of tobacco ringspot virus, and the remaining four populations failed to transmit any virus. Only one population, which transmitted all isolates, bad been associated with field spread of a nepovirus. As two California populations of Xiphinema americanum sensu lato were shown to have the ability to vector two different nepoviruses, a nematode taxonomy based on a parsimony of virus-vector re- lationship is not practical for these populations. Because two California populations ofX. americanum were able to vector tobacco ringspot virus, commonly vectored by X. americanum in the eastern United States, these western populations cannot be differentiated from eastern populations by vector capability tests using tobacco ringspot virus. Key words: dagger nematode, tobacco ringspot virus, tomato ringspot virus, nepovirus, Xiphinema americanum, Xiphinema californicum. Populations of Xiphinema americanum brownline (PBL), prunus stem pitting (PSP) Cobb, 1913 shown through rigorous test- and cherry leaf mottle (CLM) (8). Both PBL ing (23) to be nepovirus vectors include X. and PSP were transmitted with a high de- americanum sensu lato (s.1.) for tobacco gree of efficiency, whereas CLM was trans- ringspot virus (TobRSV) (5), tomato ring- mitted rarely. -
Coordinated Action of RTBV and RTSV Proteins Suppress Host RNA Silencing Machinery
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.19.427099; this version posted January 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Coordinated action of RTBV and RTSV proteins suppress host RNA silencing machinery Abhishek Anand1, Malathi Pinninti2, Anita Tripathi1, Satendra Kumar Mangrauthia2 and Neeti Sanan-Mishra1* 1 Plant RNAi Biology Group, International Center for Genetic Engineering and Biotechnology, New Delhi-110067 2 Biotechnology Section, ICAR-Indian Institute of Rice Research, Rajendranangar, Hyderabad- 500030 *Corresponding Author: Neeti Sanan-Mishra E-mail address: [email protected] Author e-mail: Abhishek Anand: [email protected] Malathi Pinninti: [email protected] Anita Tripathi: [email protected] Satendra K. Mangrauthia: [email protected] Abstract RNA silencing is as an adaptive immune response in plants that limits accumulation or spread of invading viruses. Successful virus infection entails countering the RNA silencing for efficient replication and systemic spread in the host. The viruses encode proteins having the ability to suppress or block the host silencing mechanism, resulting in severe pathogenic symptoms and diseases. Tungro virus disease caused by a complex of two viruses provides an excellent system to understand these host and virus interactions during infection. It is known that Rice tungro bacilliform virus (RTBV) is the major determinant of the disease while Rice tungro spherical virus (RTSV) accentuates the symptoms. This study brings to focus the important role of RTBV ORF-IV in Tungro disease manifestation, by acting as both the victim and silencer of the RNA silencing pathway. -
Ribozyme-Mediated Inhibition of HIV 1 Suggests Nucleolar Trafficking of HIV-1 RNA
Ribozyme-mediated inhibition of HIV 1 suggests nucleolar trafficking of HIV-1 RNA Alessandro Michienzi*, Laurence Cagnon*, Ingrid Bahner*, and John J. Rossi*†‡ *Department of Molecular Biology, Beckman Research Institute of the City of Hope, and †Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010-3011 Communicated by Arthur Landy, Brown University, Providence, RI, May 30, 2000 (received for review April 22, 2000) The HIV regulatory proteins Tat and Rev have a nucleolar localiza- Ribozymes are RNAs with catalytic activity (28). The ham- tion property in human cells. However, no functional role has been merhead ribozyme is the simplest in terms of size and structure attributed to this localization. Recently it has been demonstrated and can readily be engineered to perform intermolecular cleav- that expression of Rev induces nucleolar relocalization of some age on targeted RNA molecules. These properties make this protein factors involved in Rev export. Because the function of Rev ribozyme a useful tool for inactivating gene expression and a is to bind HIV RNA and facilitate transport of singly spliced and potential therapeutic agent. Moreover, ribozymes can be very unspliced RNA to the cytoplasm, it is likely that the nucleolus plays effective inhibitors of gene expression when they are colocalized a critical role in HIV-1 RNA export. As a test for trafficking of HIV-1 with their target RNAs (29, 30). We have taken advantage of RNAs into the nucleolus, a hammerhead ribozyme that specifically ribozyme-mediated inactivation of targeted RNAs to investigate cleaves HIV-1 RNA was inserted into the body of the U16 small whether there is nucleolar trafficking of HIV RNA. -
Multiple Origins of Prokaryotic and Eukaryotic Single-Stranded DNA Viruses from Bacterial and Archaeal Plasmids
ARTICLE https://doi.org/10.1038/s41467-019-11433-0 OPEN Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids Darius Kazlauskas 1, Arvind Varsani 2,3, Eugene V. Koonin 4 & Mart Krupovic 5 Single-stranded (ss) DNA viruses are a major component of the earth virome. In particular, the circular, Rep-encoding ssDNA (CRESS-DNA) viruses show high diversity and abundance 1234567890():,; in various habitats. By combining sequence similarity network and phylogenetic analyses of the replication proteins (Rep) belonging to the HUH endonuclease superfamily, we show that the replication machinery of the CRESS-DNA viruses evolved, on three independent occa- sions, from the Reps of bacterial rolling circle-replicating plasmids. The CRESS-DNA viruses emerged via recombination between such plasmids and cDNA copies of capsid genes of eukaryotic positive-sense RNA viruses. Similarly, the rep genes of prokaryotic DNA viruses appear to have evolved from HUH endonuclease genes of various bacterial and archaeal plasmids. Our findings also suggest that eukaryotic polyomaviruses and papillomaviruses with dsDNA genomes have evolved via parvoviruses from CRESS-DNA viruses. Collectively, our results shed light on the complex evolutionary history of a major class of viruses revealing its polyphyletic origins. 1 Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania. 2 The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA. 3 Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, 7700 Cape Town, South Africa. -
Journal of Virological Methods 153 (2008) 16–21
Journal of Virological Methods 153 (2008) 16–21 Contents lists available at ScienceDirect Journal of Virological Methods journal homepage: www.elsevier.com/locate/jviromet Use of primers with 5 non-complementary sequences in RT-PCR for the detection of nepovirus subgroups A and B Ting Wei, Gerard Clover ∗ Plant Health and Environment Laboratory, Investigation and Diagnostic Centre, MAF Biosecurity New Zealand, P.O. Box 2095, Auckland 1140, New Zealand abstract Article history: Two generic PCR protocols were developed to detect nepoviruses in subgroups A and B using degenerate Received 21 April 2008 primers designed to amplify part of the RNA-dependent RNA polymerase (RdRp) gene. It was observed that Received in revised form 17 June 2008 detection sensitivity and specificity could be improved by adding a 12-bp non-complementary sequence Accepted 19 June 2008 to the 5 termini of the forward, but not the reverse, primers. The optimized PCR protocols amplified a specific product (∼340 bp and ∼250 bp with subgroups A and B, respectively) from all 17 isolates of the 5 Keywords: virus species in subgroup A and 3 species in subgroup B tested. The primers detect conserved protein motifs Nepoviruses in the RdRp gene and it is anticipated that they have the potential to detect unreported or uncharacterised Primer flap Universal primers nepoviruses in subgroups A and B. RT-PCR © 2008 Elsevier B.V. All rights reserved. 1. Introduction together with nematode transmission make these viruses partic- ularly hard to eradicate or control (Harrison and Murant, 1977; The genus Nepovirus is classified in the family Comoviridae, Fauquet et al., 2005). -
United States Patent (10) Patent No.: US 8,759,307 B2 Stein Et Al
USOO87593 07B2 (12) United States Patent (10) Patent No.: US 8,759,307 B2 Stein et al. (45) Date of Patent: Jun. 24, 2014 (54) OLIGONUCLEOTIDE COMPOUND AND 2006/0287268 A1 12/2006 Iversen et al. ................... 514,44 METHOD FOR TREATING NIDOVIRUS 2007/0021362 A1 1/2007 Geller et al. .. 514,44 2007/0265214 A1 11/2007 Stein et al. .... ... 514/44 INFECTIONS 2009 OO88562 A1 4/2009 Weller et al. ................. 536,245 (75) Inventors: David A. Stein, Corvallis, OR (US); FOREIGN PATENT DOCUMENTS Richard K. Bestwick, Corvallis, OR (US); Patrick L. Iversen, Corvallis, OR WO WO2005/OOO234 A1 1, 2005 (US); Benjamin Neuman, Encinitas, CA WO WO2005/O13905 A1 2, 2005 (US); Michael Buchmeier, Encinitas, OTHER PUBLICATIONS CA (US); Dwight D. Weller, Corvallis, OR (US) Moulton etal Bioconjug Chem. Mar.-Apr. 2004:15(2): 290-9. Cellu lar uptake of antisense morpholino oligomers conjugated to arginine (73) Assignees: Sarepta Therapeutics, Inc., Corvallis, rich peptides.* OR (US); The Scripps Research Moulton etal AntisenseNucleic Acid Drug Dev. Feb. 2003: 13(1): 31 Institute, La Jolla, CA (US) 43. HIV Tat peptide enhances cellular delivery of antisense morpholino oligomers. (*) Notice: Subject to any disclaimer, the term of this Geller et al., Inhibition of Gene Expression in Escherichia coli by patent is extended or adjusted under 35 Antisense Phosphorodiamidate Morpholino Oligomers Antimicro U.S.C. 154(b) by 1101 days. bial Agents and Chemotherapy, Oct. 2003, p. 3233-3239, vol. 47, No. 1O.* Agrawal, S., S. H. Mayrand, et al. (1990). “Site-specific excision (21) Appl. No.: 12/109,856 from RNA by RNase H and mixed-phosphate-backbone oligodeoxynucleotides.” Proc Natl AcadSci USA, 87(4): 1401-5. -
Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies
viruses Review Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies Varvara I. Maliogka 1,* ID , Angelantonio Minafra 2 ID , Pasquale Saldarelli 2, Ana B. Ruiz-García 3, Miroslav Glasa 4 ID , Nikolaos Katis 1 and Antonio Olmos 3 ID 1 Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; [email protected] 2 Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy; [email protected] (A.M.); [email protected] (P.S.) 3 Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain; [email protected] (A.B.R.-G.); [email protected] (A.O.) 4 Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic; [email protected] * Correspondence: [email protected]; Tel.: +30-2310-998716 Received: 23 July 2018; Accepted: 13 August 2018; Published: 17 August 2018 Abstract: Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. -
Diversity of Plant Virus Movement Proteins: What Do They Have in Common?
processes Review Diversity of Plant Virus Movement Proteins: What Do They Have in Common? Yuri L. Dorokhov 1,2,* , Ekaterina V. Sheshukova 1, Tatiana E. Byalik 3 and Tatiana V. Komarova 1,2 1 Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; [email protected] (E.V.S.); [email protected] (T.V.K.) 2 Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia 3 Department of Oncology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; [email protected] * Correspondence: [email protected] Received: 11 November 2020; Accepted: 24 November 2020; Published: 26 November 2020 Abstract: The modern view of the mechanism of intercellular movement of viruses is based largely on data from the study of the tobacco mosaic virus (TMV) 30-kDa movement protein (MP). The discovered properties and abilities of TMV MP, namely, (a) in vitro binding of single-stranded RNA in a non-sequence-specific manner, (b) participation in the intracellular trafficking of genomic RNA to the plasmodesmata (Pd), and (c) localization in Pd and enhancement of Pd permeability, have been used as a reference in the search and analysis of candidate proteins from other plant viruses. Nevertheless, although almost four decades have passed since the introduction of the term “movement protein” into scientific circulation, the mechanism underlying its function remains unclear. It is unclear why, despite the absence of homology, different MPs are able to functionally replace each other in trans-complementation tests. Here, we consider the complexity and contradictions of the approaches for assessment of the ability of plant viral proteins to perform their movement function. -
Emerging Viral Diseases of Fish and Shrimp Peter J
Emerging viral diseases of fish and shrimp Peter J. Walker, James R. Winton To cite this version: Peter J. Walker, James R. Winton. Emerging viral diseases of fish and shrimp. Veterinary Research, BioMed Central, 2010, 41 (6), 10.1051/vetres/2010022. hal-00903183 HAL Id: hal-00903183 https://hal.archives-ouvertes.fr/hal-00903183 Submitted on 1 Jan 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Vet. Res. (2010) 41:51 www.vetres.org DOI: 10.1051/vetres/2010022 Ó INRA, EDP Sciences, 2010 Review article Emerging viral diseases of fish and shrimp 1 2 Peter J. WALKER *, James R. WINTON 1 CSIRO Livestock Industries, Australian Animal Health Laboratory (AAHL), 5 Portarlington Road, Geelong, Victoria, Australia 2 USGS Western Fisheries Research Center, 6505 NE 65th Street, Seattle, Washington, USA (Received 7 December 2009; accepted 19 April 2010) Abstract – The rise of aquaculture has been one of the most profound changes in global food production of the past 100 years. Driven by population growth, rising demand for seafood and a levelling of production from capture fisheries, the practice of farming aquatic animals has expanded rapidly to become a major global industry. -
Metagenomic Identification of Diverse Animal Hepaciviruses and Pegiviruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.16.100149; this version posted May 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Metagenomic identification of diverse animal hepaciviruses and 2 pegiviruses 3 4 5 Ashleigh F. Porter1, John H.-O. Pettersson1,2, Wei-Shan Chang1, Erin Harvey1, Karrie Rose3, 6 Mang Shi5, John-Sebastian Eden1,4, Jan Buchmann1, Craig Moritz6, Edward C. Holmes1 7 8 9 1. Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and 10 Environmental Sciences and School of Medical Sciences, The University of Sydney, 11 Sydney, Australia. 12 2. Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, 13 Uppsala University, Uppsala, Sweden. 14 3. Australian Registry of Wildlife Health, Taronga Conservation Society Australia, 15 Mosman, Australia. 16 4. Centre for Virus Research, Westmead Institute for Medical Research, Westmead, 17 Australia. 18 5. School of Medicine, Sun Yat-sen University, Guangzhou, China. 19 6. Research School of Biology, and Centre for Biodiversity Analysis, Australian National 20 University, Acton, ACT, Australia. 21 22 23 Address correspondence to: 24 Edward C. Holmes, 25 Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and 26 Environmental Sciences and School of Medical Sciences, The University of Sydney, 27 Sydney, Australia 28 [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.16.100149; this version posted May 17, 2020. -
The Cucumber Leaf Spot Virus P25 Auxiliary Replicase Protein Binds and Modifies the Endoplasmic Reticulum Via N-Terminal Transmembrane Domains
Virology 468-470 (2014) 36–46 Contents lists available at ScienceDirect Virology journal homepage: www.elsevier.com/locate/yviro The Cucumber leaf spot virus p25 auxiliary replicase protein binds and modifies the endoplasmic reticulum via N-terminal transmembrane domains Kankana Ghoshal a, Jane Theilmann b, Ron Reade b, Helene Sanfacon b,D’Ann Rochon a,b,n a University of British Columbia, Faculty of Land and Food Systems, Vancouver, British Columbia, Canada V6T 1Z4 b Agriculture and Agri-Food Canada Pacific Agri-Food Research Centre, 4200 Hwy 97, Summerland, British Columbia, Canada V0H 1Z0 article info abstract Article history: Cucumber leaf spot virus (CLSV) is a member of the Aureusvirus genus, family Tombusviridae. The auxiliary Received 10 June 2014 replicase of Tombusvirids has been found to localize to endoplasmic reticulum (ER), peroxisomes or Returned to author for revisions mitochondria; however, localization of the auxiliary replicase of aureusviruses has not been determined. 28 June 2014 We have found that the auxiliary replicase of CLSV (p25) fused to GFP colocalizes with ER and that three Accepted 13 July 2014 predicted transmembrane domains (TMDs) at the N-terminus of p25 are sufficient for targeting, Available online 16 August 2014 although the second and third TMDs play the most prominent roles. Confocal analysis of CLSV infected Keywords: 16C plants shows that the ER becomes modified including the formation of punctae at connections Aureusvirus between ER tubules and in association with the nucleus. Ultrastructural analysis shows that the Auxiliary replicase cytoplasm contains numerous vesicles which are also found between the perinuclear ER and nuclear Endoplasmic reticulum membrane. -
An Insect Nidovirus Emerging from a Primary Tropical Rainforest
RESEARCH ARTICLE An Insect Nidovirus Emerging from a Primary Tropical Rainforest Florian Zirkel,a,b,c Andreas Kurth,d Phenix-Lan Quan,b Thomas Briese,b Heinz Ellerbrok,d Georg Pauli,d Fabian H. Leendertz,c W. Ian Lipkin,b John Ziebuhr,e Christian Drosten,a and Sandra Junglena,c Institute of Virology, University of Bonn Medical Center, Bonn, Germanya; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USAb; Research Group Emerging Zoonosesc and Center for Biological Safety-1,d Robert Koch Institute, Berlin, Germany; and Institute of Medical Virology, Justus Liebig University Gießen, Gießen, Germanye ABSTRACT Tropical rainforests show the highest level of terrestrial biodiversity and may be an important contributor to micro- bial diversity. Exploitation of these ecosystems may foster the emergence of novel pathogens. We report the discovery of the first insect-associated nidovirus, tentatively named Cavally virus (CAVV). CAVV was found with a prevalence of 9.3% during a sur- vey of mosquito-associated viruses along an anthropogenic disturbance gradient in Côte d’Ivoire. Analysis of habitat-specific virus diversity and ancestral state reconstruction demonstrated an origin of CAVV in a pristine rainforest with subsequent spread into agriculture and human settlements. Virus extension from the forest was associated with a decrease in virus diversity (P < 0.01) and an increase in virus prevalence (P < 0.00001). CAVV is an enveloped virus with large surface projections. The RNA genome comprises 20,108 nucleotides with seven major open reading frames (ORFs). ORF1a and -1b encode two large pro- teins that share essential features with phylogenetically higher representatives of the order Nidovirales, including the families Coronavirinae and Torovirinae, but also with families in a basal phylogenetic relationship, including the families Roniviridae and Arteriviridae.