DOCSLIB.ORG

Detection and Identification of Plant Viruses Belonging to the Potyviridae

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Detection and Identification of Plant Viruses Belonging to the Potyviridae DETECTION AND IDENTIFICATION OF POTYVIRUSES AND GEMINIVIRUSES IN VIETNAM by Cuong Viet Ha Tropical Crops and Biocommodities Domain Institute of Health and Biomedical Innovation A thesis submitted for the degree of Doctor of Philosophy to the Queensland University of Technology 2007 ABSTRACT Prior to the commencement of this project, few plant viruses had been identified from Vietnam despite virus-like symptoms being commonly observed on many crops and weeds. In limited surveys in the late 1990’s, preliminary evidence was obtained indicating that potyviruses and geminiviruses were causing significant diseases. As a result, this study was aimed at developing generic PCR-based methods for the rapid detection of viruses belonging to viruses in the families Potyviridae and Geminiviridae in plant samples collected from Vietnam, and to characterise the viruses at the molecular level. Novel degenerate PCR primers were developed for the identification of begomoviruses. Using these primers, 17 begomoviruses species infecting seven crop and nine weed species in Vietnam were identified and characterised. Sequence analyses showed that ten of the viruses (six monopartite and four bipartite) were new species. Of the seven previously characterized begomoviruses, five were identified in Vietnam for the first time. Additionally, eight DNA-ß and three nanovirus-like DNA- 1 molecules were also found associated with the monopartite viruses. Five of the DNA-β molecules were putatively novel. Two novel bipartite begomoviruses, named Corchorus yellow vein virus (CoYVV) and Corchorus golden mosaic virus (CoGMV), were isolated from jute plants. Analysis of these viruses showed that they were more similar to New World begomoviruses than to viruses from the Old World. This was based on the absence of an AV2 open reading frame, the presence of an N-terminal PWRLMAGT motif in ii the coat protein and phylogenetic analysis of the DNA A and DNA B nucleotide and deduced amino acid sequences. This is the first known occurrence of Old World viruses bearing features of New World viruses, and their presence in Vietnam suggests the presence of a “New World” virus in the Old World prior to Gondwana separation. Other interesting features relating to begomoviruses identified in Vietnam were; (i) the detection of several recombination events, particularly between the newly identified Tomato yellow leaf curl Vietnam virus (TYLCVNV), and the previously characterised, Tomato leaf curl Vietnam virus (ToLCVV), (ii) the identification of new natural hosts of Sida leaf curl virus (SiLCV), Papaya leaf curl China virus (PaLCuCNV) and Alternanthera yellow vein virus (AlYVV), (iii) the first report of variation in the geminivirus stem-loop nonanucleotide sequence (CoGMV sequence was TATTATTAC rather than TAATATTAC) and (iv) the first report of different stem sequences in the stem-loop structure of two genomic components from a bipartite begomovirus, Kudzu mosaic virus (KuMV). The sequence and phylogenetic analyses of the begomoviruses and begomovirus- associated DNAs identified in this study suggested that South East Asia, and Vietnam in particular, may be a centre of begomovirus diversity. Two pairs of degenerate primers, designed in the CI gene (CIFor/CIRev) and HC-Pro gene (HPFo/HPRev), were developed for the detection of viruses in the genus Potyvirus. Using these primers, three novel potyviruses from Vietnam were detected, namely Telosma mosaic virus (TelMV) infecting telosma (Telosma cordata), Peace lily mosaic virus (PeLMV) infecting peace lily (Spathiphyllum patinii) and Wild tomato mosaic virus (WTMV) infecting wild tomato (Solanum torvum). The fragments amplified by the two sets of primers enabled additional PCR and complete iii genomic sequencing of these three viruses and a Banana bract mosaic virus (BBrMV) isolate from the Philippines. All four viruses shared genomic features typical of potyviruses. Sequence comparisons and phylogenetic analyses indicated that WTMV was most closely related to Chilli veinal mottle virus (ChiVMV) and Pepper veinal mottle virus (PVMV) while PeLMV, TelMV were related to different extents with members of the BCMV subgroup. The incidence of potyviruses infecting plants in Vietnam was investigated using the potyvirus-specific primers. Fifty two virus isolates from 13 distinct potyvirus species infecting a broad range of crops were identified in Vietnam by PCR and sequence analysis of the 3’ region of the genome. The viruses were Bean common mosaic virus (BCMV), Potato virus Y (PVY), Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV), Chilli veinal mottle virus (ChiVMV), Zucchini yellow mosaic virus (ZYMV), Leek yellow stripe virus (LYMV), Shallot yellow stripe virus (SYSV), Onion yellow dwarf virus (OYDV), Turnip mosaic virus (TuMV), Dasheen mosaic virus (DsMV), Sweet potato feathery mottle virus (SPFMV) and a novel potyvirus infecting chilli, which was tentatively named Chilli ringspot virus (ChiRSV). With the exception of BCMV and PVY, this is first report of these viruses in Vietnam. Further, rabbit bell (Crotalaria anagyroides) and typhonia (Typhonium trilobatum) were identified as new natural hosts of the Peanut stunt virus (PStV) strain of BCMV and of DsMV, respectively. Sequence and phylogenetic analyses, based on the nucleotide sequence of the entire CP-coding region of all 52 virus isolates, revealed considerable variability in BCMV, SCMV, PVY, ZYMV and DsMV. The phylogenetic analyses also suggested the possible presence of ancestral groups of BCMV, SCMV and ZYMV in Vietnam. iv Keywords: ssDNA viruses, Geminiviridae, begomovirus, ssDNA satellites, begomovirus-associated DNA β, begomovirus-associated DNA 1, ssRNA viruses, Potyviridae, potyvirus, degenerate primer, nanovirus, Vietnam. v PUBLICATIONS Publications related to this PhD thesis 1. Ha, C., Coombs, S., Revill, P., Harding, R., Vu, M., and Dale, J. (2006) Corchorus yellow vein virus, a New World geminivirus from the Old World. Journal of General Virology 87: 997-1003. 2. C. Ha, S. Coombs, P. Revill, R. Harding, M. Vu and J. Dale. (2007). Molecular characterization of begomoviruses and DNA satellites from Vietnam – additional evidence that New World geminiviruses were present in the Old World prior to continental separation. Accepted for publication in Journal of General Virology. 3. C Ha, S. Coombs, P. Revill, R. Harding, M. Vu and J. Dale. (2007). Design and application of two novel degenerate primer pairs for the detection and complete genomic characterization of potyviruses. Accepted for publication in Archives of Virology. 4. C. Ha, P. Revill, R. Harding, M. Vu and J. Dale. (2007). Identification and sequence analysis of potyviruses infecting crops in Vietnam. Accepted for publication in Archives of Virology. Papers unrelated to this PhD thesis 5. Revill, P.A., Ha, C.V., Porchun, S.C., Vu, M.T., and Dale, J.L. (2003) The complete nucleotide sequence of two distinct geminiviruses infecting cucurbits in Vietnam. Archives of Virology 148: 1523-1541. 6. Revill, P.A., Ha, C.V., Lines, R.E., Bell, K.E., Vu, M.T., and Dale, J.L. (2004) PCR and ELISA-based virus surveys of banana, papaya and cucurbit crops in Vietnam. Asia Pacific Journal of Molecular Biology and Biotechnology 12: 27 - 32. 7. Bell, K.E., Dale, J.L., Ha, C.V., Vu, M.T., and Revill, P.A. (2002) Characterisation of Rep-encoding components associated with banana bunchy top nanovirus in Vietnam. Archives of Virology 147: 695-707. vi 8. Bateson, M.F., Lines, R.E., Revill, P., Chaleeprom, W., Ha, C.V., Gibbs, A.J., and Dale, J.L. (2002) On the evolution and molecular epidemiology of the potyvirus Papaya ringspot virus. Journal of General Virology 83: 2575-2585. vii TABLE OF CONTENTS ABSTRACT.................................................................................................................ii PUBLICATIONS…………………………................................................................vi TABLE OF CONTENTS..........................................................................................viii LIST OF ABBREVIATIONS....................................................................................xii STATEMENT OF ORIGINAL AUTHORSHIP.......................................................xiv ACKNOWLEDGEMENTS.......................................................................................xv CHAPTER 1: AIMS AND OBJECTIVES………………………………………..1 CHAPTER 2: LITERATURE REVIEW……………………………………… 5 2.1. THE FAMILY GEMINIVIRIDAE ……………………………………..…… 6 2.1.1. INTRODUCTION ...........................................................................................6 2.1.2. TAXONOMY...................................................................................................6 2.1.3. GENOME ORGANIZATION.........................................................................11 2.1.3.1. Genome organization of begomoviruses.......................................................11 2.1.3.2. Genome organization of mastreviruses.........................................................15 2.1.3.3. Genome organization of curtoviruses and topocuviruses..............................16 2.1.4. FUNCTIONS OF GENES................................................................................16 2.1.4.1. Replication-associated protein (Rep).............................................................16 2.1.4.2. Coat protein (CP)...........................................................................................18 2.1.4.3. Genes on DNA-B of bipartite begomovirus..................................................21 2.1.4.4.
Load more

Recommended publications
  • Characterization of P1 Leader Proteases of the Potyviridae Family
    Characterization of P1 leader proteases of the Potyviridae family and identification of the host factors involved in their proteolytic activity during viral infection Hongying Shan Ph.D. Dissertation Madrid 2018 UNIVERSIDAD AUTONOMA DE MADRID Facultad de Ciencias Departamento de Biología Molecular Characterization of P1 leader proteases of the Potyviridae family and identification of the host factors involved in their proteolytic activity during viral infection Hongying Shan This thesis is performed in Departamento de Genética Molecular de Plantas of Centro Nacional de Biotecnología (CNB-CSIC) under the supervision of Dr. Juan Antonio García and Dr. Bernardo Rodamilans Ramos Madrid 2018 Acknowledgements First of all, I want to express my appreciation to thesis supervisors Bernardo Rodamilans and Juan Antonio García, who gave the dedicated guidance to this thesis. I also want to say thanks to Carmen Simón-Mateo, Fabio Pasin, Raquel Piqueras, Beatriz García, Mingmin, Zhengnan, Wenli, Linlin, Ruiqiang, Runhong and Yuwei, who helped me and provided interesting suggestions for the thesis as well as technical support. Thanks to the people in the greenhouse (Tomás Heras, Alejandro Barrasa and Esperanza Parrilla), in vitro plant culture facility (María Luisa Peinado and Beatriz Casal), advanced light microscopy (Sylvia Gutiérrez and Ana Oña), photography service (Inés Poveda) and proteomics facility (Sergio Ciordia and María Carmen Mena). Thanks a lot to all the assistance from lab313 colleagues. Thanks a lot to the whole CNB. Thanks a lot to the Chinese Scholarship Council. Thanks a lot to all my friends. Thanks a lot to my family. Madrid 20/03/2018 Index I CONTENTS Abbreviations………………………………………….……………………….……...VII Viruses cited…………………………………………………………………..……...XIII Summary…………………………………………………………………...….…….XVII Resumen…………………………………………………………......…...…………..XXI I.
    [Show full text]
  • Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
    Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280
    [Show full text]
  • Yellow Head Virus: Transmission and Genome Analyses
    The University of Southern Mississippi The Aquila Digital Community Dissertations Fall 12-2008 Yellow Head Virus: Transmission and Genome Analyses Hongwei Ma University of Southern Mississippi Follow this and additional works at: https://aquila.usm.edu/dissertations Part of the Aquaculture and Fisheries Commons, Biology Commons, and the Marine Biology Commons Recommended Citation Ma, Hongwei, "Yellow Head Virus: Transmission and Genome Analyses" (2008). Dissertations. 1149. https://aquila.usm.edu/dissertations/1149 This Dissertation is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Dissertations by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. The University of Southern Mississippi YELLOW HEAD VIRUS: TRANSMISSION AND GENOME ANALYSES by Hongwei Ma Abstract of a Dissertation Submitted to the Graduate Studies Office of The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2008 COPYRIGHT BY HONGWEI MA 2008 The University of Southern Mississippi YELLOW HEAD VIRUS: TRANSMISSION AND GENOME ANALYSES by Hongwei Ma A Dissertation Submitted to the Graduate Studies Office of The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Approved: December 2008 ABSTRACT YELLOW HEAD VIRUS: TRANSMISSION AND GENOME ANALYSES by I Iongwei Ma December 2008 Yellow head virus (YHV) is an important pathogen to shrimp aquaculture. Among 13 species of naturally YHV-negative crustaceans in the Mississippi coastal area, the daggerblade grass shrimp, Palaemonetes pugio, and the blue crab, Callinectes sapidus, were tested for potential reservoir and carrier hosts of YHV using PCR and real time PCR.
    [Show full text]
  • First Insight Into the Viral Community of the Cnidarian Model Metaorganism Aiptasia Using RNA-Seq Data
    First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data Jan D. Brüwer and Christian R. Voolstra Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, Saudi Arabia ABSTRACT Current research posits that all multicellular organisms live in symbioses with asso- ciated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems. To gain first insight into viruses associated with the coral model system Aiptasia (sensu Exaiptasia pallida), we analyzed an existing RNA-Seq dataset of aposymbiotic, partially populated, and fully symbiotic Aiptasia CC7 anemones with Symbiodinium. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (∼3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences could be assigned as of viral origin. Taxonomic annotation of these sequences suggests that Aiptasia is associated with a diverse viral community, comprising 116 viral taxa covering 40 families. The viral assemblage was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral assemblage, we found that some viral taxa exhibited significant changes in their relative abundance when Aiptasia engaged in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present across all conditions revealed a core virome of 15 viral taxa from 11 viral families, encompassing many viruses previously reported as members of coral viromes.
    [Show full text]
  • Ancient Recombination Events and the Origins of Hepatitis E Virus Andrew G
    Kelly et al. BMC Evolutionary Biology (2016) 16:210 DOI 10.1186/s12862-016-0785-y RESEARCH ARTICLE Open Access Ancient recombination events and the origins of hepatitis E virus Andrew G. Kelly, Natalie E. Netzler and Peter A. White* Abstract Background: Hepatitis E virus (HEV) is an enteric, single-stranded, positive sense RNA virus and a significant etiological agent of hepatitis, causing sporadic infections and outbreaks globally. Tracing the evolutionary ancestry of HEV has proved difficult since its identification in 1992, it has been reclassified several times, and confusion remains surrounding its origins and ancestry. Results: To reveal close protein relatives of the Hepeviridae family, similarity searching of the GenBank database was carried out using a complete Orthohepevirus A, HEV genotype I (GI) ORF1 protein sequence and individual proteins. The closest non-Hepeviridae homologues to the HEV ORF1 encoded polyprotein were found to be those from the lepidopteran-infecting Alphatetraviridae family members. A consistent relationship to this was found using a phylogenetic approach; the Hepeviridae RdRp clustered with those of the Alphatetraviridae and Benyviridae families. This puts the Hepeviridae ORF1 region within the “Alpha-like” super-group of viruses. In marked contrast, the HEV GI capsid was found to be most closely related to the chicken astrovirus capsid, with phylogenetic trees clustering the Hepeviridae capsid together with those from the Astroviridae family, and surprisingly within the “Picorna-like” supergroup. These results indicate an ancient recombination event has occurred at the junction of the non-structural and structure encoding regions, which led to the emergence of the entire Hepeviridae family.
    [Show full text]
  • Molecular Analysis of Vanilla Mosaic Virus from the Cook Islands
    Molecular Analysis of Vanilla mosaic virus from the Cook Islands Christopher Puli’uvea A thesis submitted to Auckland University of Technology in partial fulfilment of the requirements for the degree of Master of Science (MSc) 2017 School of Science I Abstract Vanilla was first introduced to French Polynesia in 1848 and from 1899-1966 was a major export for French Polynesia who then produced an average of 158 tonnes of cured Vanilla tahitensis beans annually. In 1967, vanilla production declined rapidly to a low of 0.6 tonnes by 1981, which prompted a nation-wide investigation with the aim of restoring vanilla production to its former levels. As a result, a mosaic-inducing virus was discovered infecting V. tahitensis that was distinct from Cymbidium mosaic virus (CyMV) and Odontoglossum ringspot virus (ORSV) but serologically related to dasheen mosaic virus (DsMV). The potyvirus was subsequently named vanilla mosaic virus (VanMV) and was later reported to infect V. tahitensis in the Cook Islands and V. planifolia in Fiji and Vanuatu. Attempts were made to mechanically inoculate VanMV to a number of plants that are susceptible to DsMV, but with no success. Based on a partial sequence analysis, VanMV-FP (French Polynesian isolate) and VanMV-CI (Cook Islands isolate) were later characterised as strains of DsMV exclusively infecting vanilla. Since its discovery, little information is known about how VanMV-CI acquired the ability to exclusively infect vanilla and lose its ability to infect natural hosts of DsMV or vice versa. The aims of this research were to characterise the VanMV genome and attempt to determine the molecular basis for host range specificity of VanMV-CI.
    [Show full text]
  • Interaction Between Zucchini Yellow Mosaic Potyvirus RNA-Dependent RNA Polymerase and Host Poly-(A) Binding Protein
    Virology 275, 433–443 (2000) doi:10.1006/viro.2000.0509, available online at http://www.idealibrary.com on View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Interaction between Zucchini Yellow Mosaic Potyvirus RNA-Dependent RNA Polymerase and Host Poly-(A) Binding Protein X. Wang,* Z. Ullah,† and R. Grumet*,†,1 *Genetics Program and †Plant Breeding and Genetics Program, Michigan State University, East Lansing, Michigan 48824 Received March 7, 2000; returned to author for revision April 7, 2000; accepted July 6, 2000 Viral replication depends on compatible interactions between a virus and its host. For RNA viruses, the viral replicases (RNA-dependent RNA polymerases; RdRps) often associate with components of the host translational apparatus. To date, host factors interacting with potyvirus replicases have not been identified. The Potyviridae, which form the largest and most economically important plant virus family, have numerous similarities with the animal virus family, the Picornaviridae. Potyviruses have a single-stranded, plus sense genome; replication initiates at the viral-encoded, 3Ј poly-(A) terminus. The yeast two-hybrid system was used to identify host plant proteins associating with the RdRp of zucchini yellow mosaic potyvirus (ZYMV). Several cDNA clones representing a single copy of a poly-(A) binding protein (PABP) gene were isolated from a cucumber (Cucumis sativus L.) leaf cDNA library. Deletion analysis indicated that the C-terminus of the PABP is necessary and sufficient for interaction with the RdRp. Full-length cucumber PABP cDNA was obtained using 5Ј RACE; in vitro and Escherichia coli-expressed PABP bound to poly-(A)–Sepharose and ZYMY RdRp with or without the presence of poly-(A).
    [Show full text]
  • Characterization of a New Potyvirus Causing Mosaic and Flower Variegation in Catharanthus Roseus in Brazil
    New potyvirus causing mosaic and fl ower variegation in C. roseus 687 Note Characterization of a new potyvirus causing mosaic and fl ower variegation in Catharanthus roseus in Brazil Sheila Conceição Maciel1, Ricardo Ferreira da Silva1, Marcelo Silva Reis2, Adriana Salomão Jadão3, Daniel Dias Rosa1, José Segundo Giampan4, Elliot Watanabe Kitajima3, Jorge Alberto Marques Rezende3*, Luis Eduardo Aranha Camargo3 1USP/ESALQ – Programa de Pós-Graduação em Fitopatologia. 2Centro de Citricultura Sylvio Moreira/Bioinformática – 13490-970 – Cordeirópolis, SP – Brasil. 3USP/ESALQ – Depto. de Fitopatologia e Nematologia – C.P. 09 – 13418-900 – Piracicaba, SP – Brasil. 4IAPAR – Área de Proteção de Plantas – C.P. 481 - 86047-902 – Londrina, PR – Brasil. *Corresponding author <[email protected]> Edited by: Luís Reynaldo Ferracciú Alleoni ABSTRACT: Catharanthus roseus is a perennial, evergreen herb in the family Apocynaceae, which is used as ornamental and for popular medicine to treat a wide assortment of human diseases. This paper describes a new potyvirus found causing mosaic symptom, foliar malformation and flower variegation in C. roseus. Of 28 test-plants inoculated mechanically with this potyvirus, only C. roseus and Nicotiana benthamiana developed systemic mosaic, whereas Chenopodium amaranticolor and C. quinoa exhibited chlorotic local lesions. The virus was transmitted by Aphis gossypii and Myzus nicotianae. When the nucleotide sequence of the CP gene (768nt) was compared with other members of the Potyviridae family, the highest identities varied from 67 to 76 %. For the 3' UTR (286nt), identities varied from 16.8 to 28.6 %. The name Catharanthus mosaic virus (CatMV) is proposed for this new potyvirus. Keywords: RT-PCR, Apocynaceae, periwinkle, diagnose, genome sequencing Introduction Cucumis sativus, Cucurbita pepo cv.
    [Show full text]
  • Unconventional Viral Gene Expression Mechanisms As Therapeutic Targets
    Review Unconventional viral gene expression mechanisms as therapeutic targets https://doi.org/10.1038/s41586-021-03511-5 Jessica Sook Yuin Ho1,3, Zeyu Zhu1,3 & Ivan Marazzi1,2 ✉ Received: 8 June 2020 Accepted: 22 March 2021 Unlike the human genome that comprises mostly noncoding and regulatory sequences, Published online: 19 May 2021 viruses have evolved under the constraints of maintaining a small genome size while expanding the efciency of their coding and regulatory sequences. As a result, viruses Check for updates use strategies of transcription and translation in which one or more of the steps in the conventional gene–protein production line are altered. These alternative strategies of viral gene expression (also known as gene recoding) can be uniquely brought about by dedicated viral enzymes or by co-opting host factors (known as host dependencies). Targeting these unique enzymatic activities and host factors exposes vulnerabilities of a virus and provides a paradigm for the design of novel antiviral therapies. In this Review, we describe the types and mechanisms of unconventional gene and protein expression in viruses, and provide a perspective on how future basic mechanistic work could inform translational eforts that are aimed at viral eradication. Expression of a gene in the human genome is a multistep and heavily (for example, alternative splicing) or use unique strategies. Here we regulated process that resembles a production line. Protein-coding describe the diverse ways by which viral genomes give rise to genes and genes are transcribed almost exclusively by RNA polymerase II (RNAPII). proteins that deviate from the canonical framework of human genes, During transcription, quality-control checkpoints are implemented to restricting our analyses to eukaryotes and their viruses.
    [Show full text]
  • The Induction of Infectivity in Human Astrovirus in Response to Capsid
    ABSTRACT The Induction of Infectivity in Human Astrovirus in Response to Capsid Proteolysis by Justin Harper Astrovirus is a non-enveloped, T=3, positive-sense RNA virus that presents with self-limiting gastroenteritis; however, it has been additionally associated with serious presentations such as nephritis, hepatitis, and encephalitis, which is compounded by its propensity to engage in cross-species penetrations. Astrovirus undergoes a complex capsid maturation process mediated by host proteases in which an inert, immature capsid composed of VP90 is sequentially cleaved to yield a highly infectious particle composed of VP34 and VP27/VP25, which form the capsid shell and spikes, respectively. By overexpressing a VP9070-418 truncate in insect cells, we have demonstrated that the shell domain alone cannot support particle assembly, implying a crucial role for the dimeric contacts within the spike. Various monomeric, shell domain truncates (i.e. VP9071-252, VP9071-283, VP9071-313, and VP9071-415) have been successfully expressed and purified, but none yielded useful crystals, suggesting the structural context of the capsid lattice may be needed to stabilize their conformational flexibility. Acknowledgments There are many people deserving of my gratitude, without which this work would have been nigh impossible. Foremost, I need to acknowledge my thesis adviser Jane Tao whose guidance and knowledge of structural virology has been critical in providing direction and spurring ideas regarding novel ways to surmount my encountered difficulties. There are also the members of the Tao and Shamoo lab who have provided an array of technical expertise, troubleshooting, and conversations that have guided this research: Haijiang Chen, Aaron Collier, Milya Davlieva, Yangyang Dong, Yusong Guo, Tom Guu, Yukimatsu Toh, and Wenjie Zheng.
    [Show full text]
  • Protein-RNA Linkage and Posttranslational Modifications of Feline Calicivirus and Murine Norovirus Vpg Proteins
    A peer-reviewed version of this preprint was published in PeerJ on 28 June 2016. View the peer-reviewed version (peerj.com/articles/2134), which is the preferred citable publication unless you specifically need to cite this preprint. Olspert A, Hosmillo M, Chaudhry Y, Peil L, Truve E, Goodfellow I. 2016. Protein-RNA linkage and posttranslational modifications of feline calicivirus and murine norovirus VPg proteins. PeerJ 4:e2134 https://doi.org/10.7717/peerj.2134 1 Protein-RNA linkage and posttranslational modifications of feline calicivirus and 2 murine norovirus VPg proteins 3 4 Authors: 1 2 2 3 1 5 Allan Olspert , Myra Hosmillo , Yasmin Chaudhry , Lauri Peil , Erkki Truve and Ian 2* 6 Goodfellow 7 8 1) Faculty of Science, Department of Gene Technology, Tallinn University of Technology, 9 Akadeemia tee 15, 12618 Tallinn, Estonia 10 2) Division of Virology, Department of Virology, University of Cambridge, Addenbrooke’s 11 Hospital, Hills Road, Cambridge, UK 12 3) Faculty of Science and Technology, Institute of Technology, University of Tartu, Nooruse 13 1, 50411 Tartu, Estonia 14 15 *Corresponding author 16 Ian Goodfellow 17 Division of Virology, Department of Virology, University of Cambridge, Addenbrooke’s 18 Hospital, Hills Road, Cambridge, UK 19 Email: [email protected] PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.1960v1 | CC-BY 4.0 Open Access | rec: 14 Apr 2016, publ: 14 Apr 2016 20 Abstract (max 500 words):302 21 Members of the Caliciviridae family of positive sense RNA viruses cause a wide range of 22 diseases in both humans and animals. The detailed characterization of the calicivirus life cycle 23 had been hampered due to the lack of robust cell culture systems and experimental tools for 24 many of the members of the family.
    [Show full text]
  • Structure of Flexible Filamentous Plant Virusesᰔ Amy Kendall,1 Michele Mcdonald,1 Wen Bian,1 Timothy Bowles,1 Sarah C
    JOURNAL OF VIROLOGY, Oct. 2008, p. 9546–9554 Vol. 82, No. 19 0022-538X/08/$08.00ϩ0 doi:10.1128/JVI.00895-08 Copyright © 2008, American Society for Microbiology. All Rights Reserved. Structure of Flexible Filamentous Plant Virusesᰔ Amy Kendall,1 Michele McDonald,1 Wen Bian,1 Timothy Bowles,1 Sarah C. Baumgarten,1 Jian Shi,2† Phoebe L. Stewart,2 Esther Bullitt,3 David Gore,4 Thomas C. Irving,4 Wendy M. Havens,5 Said A. Ghabrial,5 Joseph S. Wall,6 and Gerald Stubbs1* Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 372351; Department of Molecular Physiology and Biophysics and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 372322; Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 021183; BioCAT, CSRRI, and BCPS, Illinois Institute of Technology, Chicago, Illinois 604394; Plant Pathology Department, University of Kentucky, Lexington, Kentucky 405465; and Biology Department, Brookhaven National Laboratory, Upton, New York 119736 Received 29 April 2008/Accepted 17 July 2008 Flexible filamentous viruses make up a large fraction of the known plant viruses, but in comparison with those of other viruses, very little is known about their structures. We have used fiber diffraction, cryo-electron microscopy, and scanning transmission electron microscopy to determine the symmetry of a potyvirus, soybean mosaic virus; to confirm the symmetry of a potexvirus, potato virus X; and to determine the low-resolution structures of both viruses. We conclude that these viruses and, by implication, most or all flexible filamentous plant viruses share a common coat protein fold and helical symmetry, with slightly less than 9 subunits per helical turn.
    [Show full text]