Protein Structure-Guided Hidden Markov Models (Hmms) As a Powerful Method in the Detection of Ancestral Endogenous Viral Elements
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Comparison of Plant‐Adapted Rhabdovirus Protein Localization and Interactions
University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2011 COMPARISON OF PLANT‐ADAPTED RHABDOVIRUS PROTEIN LOCALIZATION AND INTERACTIONS Kathleen Marie Martin University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Martin, Kathleen Marie, "COMPARISON OF PLANT‐ADAPTED RHABDOVIRUS PROTEIN LOCALIZATION AND INTERACTIONS" (2011). University of Kentucky Doctoral Dissertations. 172. https://uknowledge.uky.edu/gradschool_diss/172 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Kathleen Marie Martin The Graduate School University of Kentucky 2011 COMPARISON OF PLANT‐ADAPTED RHABDOVIRUS PROTEIN LOCALIZATION AND INTERACTIONS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Kathleen Marie Martin Lexington, Kentucky Director: Dr. Michael M Goodin, Associate Professor of Plant Pathology Lexington, Kentucky 2011 Copyright © Kathleen Marie Martin 2011 ABSTRACT OF DISSERTATION COMPARISON OF PLANT‐ADAPTED RHABDOVIRUS PROTEIN LOCALIZATION AND INTERACTIONS Sonchus yellow net virus (SYNV), Potato yellow dwarf virus (PYDV) and Lettuce Necrotic yellows virus (LNYV) are members of the Rhabdoviridae family that infect plants. SYNV and PYDV are Nucleorhabdoviruses that replicate in the nuclei of infected cells and LNYV is a Cytorhabdovirus that replicates in the cytoplasm. LNYV and SYNV share a similar genome organization with a gene order of Nucleoprotein (N), Phosphoprotein (P), putative movement protein (Mv), Matrix protein (M), Glycoprotein (G) and Polymerase protein (L). -
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. -
Corona and Other Virus: Their Useful and Harmful Aspects
Current Trends on Biotechnology & Microbiology DOI: ISSN: 2641-6875 10.32474/CTBM.2020.02.000129Review Article Corona and Other Virus: Their Useful and Harmful Aspects Birhanu Gizaw* Microbial Biodiversity Directorate, Ethiopian Biodiversity Institute, Ethiopia *Corresponding author: Birhanu Gizaw, Microbial Biodiversity Directorate, Ethiopian Biodiversity Institute, P.O. Box 30726, Addis Ababa, Ethiopia Received: June 15, 2020 Published: September 22, 2020 Abstract How the single virus is forceful and shakes the world is eyewitness during this contemporary COVID 19 pandemic time. People primarily think of viruses such as HIV, Ebola, Zika, Influenza, Tobacco mosaic virus or whatever new outbreak like SARS, Corona are Understandingall viruses worst the and microbial non-beneficial. world isHowever, very critical not all and viruses crucial are thing detrimental that they and are influential driving force to human, and governing animal and the plantphysical health. world In fact, some viruses have beneficial properties for their hosts in a symbiotic relationship and scientific research in many disciplines. industry,and biosphere agriculture, at all. Thehealth virus and and environment other microbial are the life application those of bacteria, of microbes fungi, andprion, their viroid, products virion are are too requiring high for great human attention being and researchenvironment. to enhance Without their microbes utilization all lifefrom would majority be cease of useful on earth.aspects However, of microbial some genetic microbes resource. are very The dangerous secret behind like of Corona every virus, HIV, Ebola, Mycobacterium and others that destroy human life, but majority of microorganisms are too useful to promote virusdevelopment. in respect Through with health, building environment, and strengthening agriculture microbial and biotechnological culture collection application centers during and through this Covid19 strong pandemic conservation time strategy, to raise awarenessit is possible about to exploit virus atmore all. -
Nucleotide Sequence and Phylogenetic Analysis of a Bamboo Mosaic Potexvirus Isolate from Common Bamboo (Bambusa Vulgaris Mcclure)
YangBot. Bull. et al. Acad. Nucleotide Sin. (1997) sequence 38: 77-84 of BaMV-V RNA 77 Nucleotide sequence and phylogenetic analysis of a bamboo mosaic potexvirus isolate from common bamboo (Bambusa vulgaris McClure) Chi-Chen Yang1,2, Jih-Shiou Liu1, Chan-Pin Lin2 and Na-Sheng Lin1,3 1Institute of Botany, Academia Sinica, Taipei, Taiwan 115, Republic of China 2Department of Plant Pathology and Entomology, National Taiwan University, Taipei, Taiwan, Republic of China (Received September 20, 1996; Accepted January 30, 1997) Abstract. The complete cDNA sequence corresponding to the genomic RNA of an isolate bamboo mosaic potexvirus (BaMV-V) from common bamboo (Bambusa vulgaris McClure) was determined. This isolate is the first potexvirus with which a satellite RNA has been associated. The genome organization of BaMV-V, similar to those of other potexviruses, contained five open reading frames (ORFs 15) coding for polypeptides with molecular weight of 156 kDa, 28 kDa, 13 kDa, 6 kDa, and 25 kDa, respectively. Nucleotide sequence analysis showed a 10.0% difference from the BaMV-O isolate previously described whereas the amino acid comparison showed a difference of 3.2%. When three conservative domains of RNA dependent RNA polymerase (RdRp) were used for phylogenetic analysis, the greatest variation between two strains of each virus was only 12.8% of that between the two closest members of the potexvirus group. The grouping of potexviruses distinct from other groups of plant viruses was also confirmed by a comparision of three conservative motifs of RdRp. Keywords: Bamboo mosaic virus; Nucleotide sequence; Potexvirus. Introduction virus M, PVM) (Zavriev et al., 1991), hordeivirus (e.g. -
Tamada-Text R3 HK-TT
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Okayama University Scientific Achievement Repository Tamada & Kondo - 1 Journal of General Plant Pathology Biological and genetic diversity of plasmodiophorid-transmitted viruses and their vectors Tetsuo Tamada* and Hideki Kondo Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan. Current address for T. Tamada: Kita 10, Nishi 1, 13-2-606, Sapporo, 001-0010, Japan. *Corresponding author: Tetsuo Tamada; E-mail: [email protected] Total text pages 32 Word counts: 10 words (title); 147 words (Abstract); 6004 words (Main Text) Tables: 3; Figure: 1; Supplementary figure: 1 Tamada & Kondo - 2 Abstract About 20 species of viruses belonging to five genera, Benyvirus, Furovirus, Pecluvirus, Pomovirus and Bymovirus, are known to be transmitted by plasmodiophorids. These viruses have all positive-sense single-stranded RNA genomes that consist of two to five RNA components. Three species of plasmodiophorids are recognized as vectors: Polymyxa graminis, P. betae, and Spongospora subterranea. The viruses can survive in soil within the long-lived resting spores of the vector. There are biological and genetic variations in both virus and vector species. Many of the viruses have become the causal agents of important diseases in major crops, such as rice, wheat, barley, rye, sugar beet, potato, and groundnut. Control measure is dependent on the development of the resistant cultivars. During the last half a century, several virus diseases have been rapidly spread and distributed worldwide. For the six major virus diseases, their geographical distribution, diversity, and genetic resistance are addressed. -
The Development and Characterisation of Grapevine Virus-Based
The development and characterisation of grapevine virus-based expression vectors by Jacques du Preez Presented in partial fulfilment of the requirements for the degree Doctor of Philosophy at the Department of Genetics, Stellenbosch University March 2010 Supervisors: Prof JT Burger and Dr DE Goszczynski Study leader: Dr D Stephan Declaration I, the undersigned, hereby declare that the work contained in this thesis is my own original work and that I have not previously in its entirety or in part submitted it at any university for a degree. ______________________ Date: _______________ Jacques du Preez Copyright © 2010 Stellenbosch University All rights reserved ii Abstract Grapevine ( Vitis vinifera L.) is a very important agricultural commodity that needs to be protected. To achieve this several in vivo tools are needed for the study of this crop and the pathogens that infect it. Recently the grapevine genome has been sequenced and the next important step will be gene annotation and function using these in vivo tools. In this study the use of Grapevine virus A (GVA), genus Vitivirus , family Flexiviridae , as transient expression and VIGS vector for heterologous protein expression and functional genomics in Nicotiana benthamiana and V . vinifera were evaluated. Full-length genomic sequences of three South African variants of the virus (GTR11, GTG111 and GTR12) were generated and used in a molecular sequence comparison study. Results confirmed the separation of GVA variants into three groups, with group III (mild variants) being the most distantly related. It showed the high molecular heterogeneity of the virus and that ORF 2 was the most diverse. The GVA variants GTG111, GTR12 and GTR11 were placed in molecular groups I, II and III respectively. -
Small Hydrophobic Viral Proteins Involved in Intercellular Movement of Diverse Plant Virus Genomes Sergey Y
AIMS Microbiology, 6(3): 305–329. DOI: 10.3934/microbiol.2020019 Received: 23 July 2020 Accepted: 13 September 2020 Published: 21 September 2020 http://www.aimspress.com/journal/microbiology Review Small hydrophobic viral proteins involved in intercellular movement of diverse plant virus genomes Sergey Y. Morozov1,2,* and Andrey G. Solovyev1,2,3 1 A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia 2 Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia 3 Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia * Correspondence: E-mail: [email protected]; Tel: +74959393198. Abstract: Most plant viruses code for movement proteins (MPs) targeting plasmodesmata to enable cell-to-cell and systemic spread in infected plants. Small membrane-embedded MPs have been first identified in two viral transport gene modules, triple gene block (TGB) coding for an RNA-binding helicase TGB1 and two small hydrophobic proteins TGB2 and TGB3 and double gene block (DGB) encoding two small polypeptides representing an RNA-binding protein and a membrane protein. These findings indicated that movement gene modules composed of two or more cistrons may encode the nucleic acid-binding protein and at least one membrane-bound movement protein. The same rule was revealed for small DNA-containing plant viruses, namely, viruses belonging to genus Mastrevirus (family Geminiviridae) and the family Nanoviridae. In multi-component transport modules the nucleic acid-binding MP can be viral capsid protein(s), as in RNA-containing viruses of the families Closteroviridae and Potyviridae. However, membrane proteins are always found among MPs of these multicomponent viral transport systems. -
Disruption of Virus Movement Confers Broad-Spectrum Resistance Against
Proc. Nati. Acad. Sci. USA Vol. 91, pp. 10310-10314, October 1994 Plant Biology Disruption of virus movement confers broad-spectrum resistance against systemic infection by plant viruses with a triple gene block (trnenic plant/doinat negative mutaton/ n l movement proein) DAVID L. BECK, CRAIG J. VAN DOLLEWEERD, TONY J. LOUGH, EZEQUIEL BALMORI, DAVIN M. VOOT, MARK T. ANDERSEN, IONA E. W. O'BRIEN, AND RICHARD L. S. FORSTERt Molecular Genetics Group, The Horticultural and Food Research Institute of New Zealand Ltd., Private Bag 92169, Auckland, New Zealand Communicated by George Bruening, June 23, 1994 ABSTRACT White clover mosaic virus strain 0 (WCIMV- tially difficult. New forms ofresistance active against several 0), species of the Potexvirus genus, contains a set of three different viruses or groups of viruses are being sought. One partially overlapping genes (the triple gene block) that encodes such approach involved the introduction of the gene coding nonvirion proteins of 26 kDa, 13 kDa, and 7 kDa. These for rat 2'-5' oligoadenylate synthetase into the genome of proteins are necesy for cell-to-cell movement in plants but potato plants (4). Genetically engineering transgenic plants to not for replication. The WCIMV-O 13-kDa gene was mutated block virus movement, mimicking the mechanism of some (to 13*) in a region of the gene that is conserved in all viruses natural resistance genes, has been proposed (1, 5, 6) but known to possess triple-gene-block proteins. All 10 13* trans- remains mostly unexploited. genic lines of Nicodiana benthamiana designed to express the The movement function of plant viruses can be comple- mutated movement protein were shown to be resistant to mented by another, frequently unrelated, virus in double systemic infection by WCIMV-O at 1 jug ofWCIMV virions per infections (7). -
Plant-Based Vaccines: the Way Ahead?
viruses Review Plant-Based Vaccines: The Way Ahead? Zacharie LeBlanc 1,*, Peter Waterhouse 1,2 and Julia Bally 1,* 1 Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia; [email protected] 2 ARC Centre of Excellence for Plant Success in Nature and Agriculture, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia * Correspondence: [email protected] (Z.L.); [email protected] (J.B.) Abstract: Severe virus outbreaks are occurring more often and spreading faster and further than ever. Preparedness plans based on lessons learned from past epidemics can guide behavioral and pharmacological interventions to contain and treat emergent diseases. Although conventional bi- ologics production systems can meet the pharmaceutical needs of a community at homeostasis, the COVID-19 pandemic has created an abrupt rise in demand for vaccines and therapeutics that highlight the gaps in this supply chain’s ability to quickly develop and produce biologics in emer- gency situations given a short lead time. Considering the projected requirements for COVID-19 vaccines and the necessity for expedited large scale manufacture the capabilities of current biologics production systems should be surveyed to determine their applicability to pandemic preparedness. Plant-based biologics production systems have progressed to a state of commercial viability in the past 30 years with the capacity for production of complex, glycosylated, “mammalian compatible” molecules in a system with comparatively low production costs, high scalability, and production flexibility. Continued research drives the expansion of plant virus-based tools for harnessing the full production capacity from the plant biomass in transient systems. -
Us 2012/0074.014 A1 2 .. 1
US 2012O074O14A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0074.014 A1 Tran et al. (43) Pub. Date: Mar. 29, 2012 (54) PRODUCT TYPICALLY BASED ON SALT OF Publication Classification PEROXYMONOSULFURIC ACID AND (51) Int. Cl SUITABLE FOR MEDICINAL USAGE, AND iBio/02 (2006.01) ASSOCATED PRODUCT FABRICATION B23P 19/00 (2006.01) A633/42 (2006.01) (75) Inventors: David Van Tran, San Jose, CA A6IR 9/14 (2006.01) (US); David Nguyen Tran, San CD7C 409/244 (2006.01) Jose, CA (US) A6II 3/327 (2006.01) s (52) U.S. Cl. ............. 206/438: 562/1; 514/578; 424/605; 424/400; 29/428 (73) Assignee: LuTran Industries, Inc. (57) ABSTRACT 21) Appl. No.: 13AO47,742 Products based on salt of peroxyperoxVmonosulfuric acid are suit (21) Appl. No 9 able for treating or/and preventing diseases and other debili tating medical conditions caused by bacterial, eukaryotic, (22) Filed: Mar. 14, 2011 prion, and viral pathogens and by non-pathogenic inflamma tion. The products may alternatively be based on inorganic Related U.S. Application Data halide and an oxidizing agent reactable in water with the inorganic halide to generate hypohalite ions. In addition, the (60) Provisional application No. 61/386,928, filed on Sep. products can be employed in other applications such as com 27, 2010. mercial and industrial applications. 5T. 2 .. 2. 1.4. J., Patent Application Publication Mar. 29, 2012 Sheet 1 of 2 US 2012/0074014 A1 cro Q-D 22 Fig. 2a Fig.2b Patent Application Publication Mar. 29, 2012 Sheet 2 of 2 US 2012/0074014 A1 90 92 US 2012/0074014 A1 Mar. -
Progress and Prospects of Studies on Polymyxa Graminis and Its Transmitted Cereal Viruses in China*
PROGRESS IN NATURAL SCIENCE V ol .15 , No .6 , June 2005 REVIEW ARTICLE Progress and prospects of studies on Polymyxa graminis and its transmitted cereal viruses in China* CH EN Jianping ** (Virology and Biotechnology Institute , Zhejiang Academy of Agricultural Sciences, Key Laboratory of Plant Virology , Ministry of Agri- culture and Zhejiang Province, Hangzhou 310021, China) Received October 8 , 2004 ;revised October 25 , 2004 Abstract Polymyxa gram inis is a eukaryotic obligate biotrophic parasite of plant roots that belongs to a poorly studied discrete taxonomic unit informally called “ plasmodiophorids” .P .graminis is nonpathogenic , but has the ability to acquire and transmit nine plant viruses w hich belong to genera Bymovirus and Furovirus and cause serious diseases in cereal crop speciesand also result in significant yield reductions in China and elsew here.Genus Bymovirus contains barley yellow mosaic virus (BaYMV), barley mild mosaic virus (BaMMV), w heat yellow mosaic virus (WYMV), w heat spindle streak mosaic virus (WSS MV), and oat mosaic virus (OMV), and genus F urovirus contains soil-borne w heat mosaic virus(S BW MV), oat golden stripe virus(OGSV), and new ly identified Chinese w heat mosaic virus(CWM V)and soil-borne cereal mosaic virus(S BCMV).All these viruses have been sequenced and their w orldw ide distribu- tions have been studied .The viruses are protected by the environment w ithin P .gra minis resting spores that may remain dormant but vi- able for decades(probably until a suitable host plant is encountered).S pontaneous deletion mutants of S BW MV , OGS V and OMV are de- tected , and these deletion mutants are not transmissible by the fungus.The persistent, soil-borne nature of these diseases makes the use of virus-resistant crop varieties cu rren tly the only practical and environmentally friendly means to control them , and a large number of disease resistant germ plasms have been screened . -
(12) Patent Application Publication (10) Pub. No.: US 2009/0069256A1 Smith Et Al
US 20090069256A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2009/0069256A1 Smith et al. (43) Pub. Date: Mar. 12, 2009 (54) ENHANCING PROTEIN EXPRESSION Related U.S. Application Data (60) Provisional application No. 60/576,819, filed on Jun. (76) Inventors: Larry R. Smith, San Diego, CA 4, 2004. (US); Vafa Shahabi, Valley Forge, PA (US); Maninder K. Sidhu, New Publication Classification City, NY (US) (51) Int. Cl. A63L/7088 (2006.01) Correspondence Address: CI2N IS/II (2006.01) HUNTON & WILLIAMS LLP CI2N 15/87 (2006.01) INTELLECTUAL PROPERTY DEPARTMENT A6IP 43/00 (2006.01) 1900 KSTREET, N.W., SUITE 1200 CI2N IS/00 (2006.01) WASHINGTON, DC 20006-1109 (US) (52) U.S. Cl. ...... 514/44; 536/23.1; 536/23.53: 536/23.5; 536/23.6:536/23.7:536/23.72:536/23.74; 435/455; 435/320.1 (21) Appl. No.: 11/628,455 (57) ABSTRACT (22) PCT Fled: Jun. 6, 2005 Modified polynucleotide compositions providing enhanced gene expression and methods for preparing said compositions (86) PCT NO.: PCT/US05/19592 are disclosed. Methods of using the compositions, such as in screening assays, diagnostic tools, kits, etc. and for preven S371 (c)(1), tion and/or treatment of diseases and disorders are also dis (2), (4) Date: Nov. 8, 2007 closed. SWall (3733) DraI(3734) Stul (52) BclI (3512) ASCI (3496) ApaI (3482) BSInI (3370) BglII (457) 2->BGHpolyA BspEI (3271) BspMI (540) BseRI (3241) human IL-15 (BH15) Psp1406I (667) BamHI (3071) “HuigE leader PflMI (3056) kanamycin Eael (768) NsiI (791) (3737 bp) XmnI (806) BpmI (2976)1 AgeI (846) MsiI (2745) BSrFI (846) SnaBI (2722) Eam1105I (920) BSaAI (2722) DraII (1155) Asel (2390) Spel (2383) EcoRV (2291) ClaI (2285) NruI (2254) BSrBI (1965) AfilII (1896) MunI (2209) Patent Application Publication Mar.