DOCSLIB.ORG

Sequencing and Analysis of the Complete Genome of Rana Grylio Virus (RGV)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Sequencing and Analysis of the Complete Genome of Rana Grylio Virus (RGV) Arch Virol (2012) 157:1559–1564 DOI 10.1007/s00705-012-1316-9 BRIEF REPORT Sequencing and analysis of the complete genome of Rana grylio virus (RGV) Xiao-Ying Lei • Tong Ou • Ruo-Lin Zhu • Qi-Ya Zhang Received: 13 February 2012 / Accepted: 19 March 2012 / Published online: 28 April 2012 Ó Springer-Verlag 2012 Abstract Infection with Rana grylio virus (RGV), an including the genera Iridovirus, Chloriridovirus, Lympho- iridovirus isolated in China in 1995, resulted in a high cystivirus, Megalocytivirus and Ranavirus [4]. So far, the mortality rate in frogs. The complete genome sequence of entire genomes of 18 iridoviruses have been sequenced RGV was determined and analyzed. The genomic DNA completely (Table S1). Three of these are invertebrate- was 105,791 bp long, with 106 open reading frames infecting iridoviruses, and the other 15 are associated with (ORFs). Dot plot analysis showed that the gene order of aquatic vertebrates. These include lymphocystis disease RGV shared colinearity with three completely sequenced virus 1 (LCDV-1) and lymphocystis disease virus-China ranaviruses. A phylogenetic tree was constructed based on (LCDV-C), belonging to the genus Lymphocystivirus, and concatenated sequences of iridovirus 26 core-gene-encoded infectious spleen and kidney necrosis virus (ISKNV), rock proteins, and the result showed high bootstrap support for bream iridovirus (RBIV), turbot reddish body iridovirus RGV being a member of the genus Ranavirus and that (TRBIV), and other viruses, belonging to the genus Mega- iridoviruses of other genera also clustered closely. A locytivirus that can infect fish species. Iridoviruses of the microRNA (miRNA) prediction revealed that RGV could genus Ranavirus, including frog virus 3 (FV3), soft-shelled encode 18 mature miRNAs, many of which were located turtle iridovirus (STIV), epizootic hematopoietic necrosis near genes associated with virus replication. Thirty-three virus (EHNV), and other viruses can infect amphibians, repeated sequences were found in the RGV genome. fish and reptiles [5–12]. These results provide insight into the genetic nature of Members of the genus Ranavirus have been recognized RGV and are useful for laboratory diagnosis for vertebrate as major pathogens of economically and ecologically iridoviruses. important cold-blooded vertebrates and have become seri- ous problems in modern aquaculture, fish farming, and wildlife conservation because of their epidemic morbidity Iridoviruses are nucleo-cytoplasmic large DNA viruses and ability to cause mortality [13]. Rana grylio virus (NCLDVs) and contain circularly permutated and termi- (RGV) is a pathogenic agent that results in greater than nally redundant double-stranded genomes [1–3]. The 90 % mortality in cultured pig frog (Rana grylio), which family Iridoviridae currently contains five genera, was the first iridovirus isolated in China in 1995 [14, 15]. RGV has been recognized as a member of the family Iri- doviridae and is closely related to FV3, based on previous Electronic supplementary material The online version of this studies on morphogenesis, cellular interaction, antigenicity, article (doi:10.1007/s00705-012-1316-9) contains supplementary restriction fragment length polymorphism (RFLP) and material, which is available to authorized users. major capsid protein (MCP) sequence similarity [15–18]. X.-Y. Lei Á T. Ou Á R.-L. Zhu Á Q.-Y. Zhang (&) To date, some genes of RGV have been identified and State Key Laboratory of Freshwater Ecology and Biotechnology, characterized, such as 3b-hydroxysteroid dehydrogenase Institute of Hydrobiology, Chinese Academy of Sciences, (3b-HSD), deoxyuridine triphosphatase (dUTPase), an Graduate School of the Chinese Academy of Sciences, Wuhan 430072, China envelope protein gene (53R), thymidine kinase (TK) and e-mail: [email protected] a gene belonging to the ‘‘essential for respiration and 123 1560 X.-Y. Lei et al. Fig. 1 Organization of the RGV genome. Predicted ORFs are of methionine start and stop codons. Black arrows represent the ORFs numbered from left to right and represented by arrows indicating with predicted functions, and the white ones represent those with their approximate size, location and orientation based on the positions unknown function viability’’ family (ERV1) [19–24]. We found that RGV studied previously were not amplified again. All of the could induce apoptosis mediated by mitochondria [25]. fragments were purified using a TIANgel Mini Purification RGV has the potential to be used as a viral vector for Kit (Tiangen Biotech), cloned into vector pMD18-T expression of foreign genes in fish cells [26]. (TaKaRa), and sequenced in both directions in an ABI PRISM So far, the complete sequence of RGV has not been 3700 automated DNA sequencer using M13 primers. available, and the relationship of RGV to other iridoviruses Genomic DNA assembly, structure analysis, and amino has not been well understood. To aid in the understanding acid sequence analysis were carried out using the DNA- of the molecular mechanisms of amphibian iridovirus STAR software package (Lasergene, Madison, WI, USA). pathogenesis and its evolutionary status, the complete The ORFs were predicted using Gene Finding in the virus sequence of RGV genomic DNA was determined and genome program at the website http://www.softberry.com analyzed. and NCBI ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/ RGV was isolated from tissues of diseased young pig gorf.html). Comparisons of homologous protein-encoding frogs with lethal syndrome in Hubei Province, China, in regions of RGV with those of other viruses were conducted 1995, and Epithelioma papulosum cyprinid (EPC) cells using the BLASTP program at NCBI website (http://www. were used for virus propagation, grown in TC 199 medium ncbi.nlm.nih.gov). Transmembrane domains (TMs) were supplemented with 10 % fetal bovine serum (FBS) at predicted using TMHMM 2.0 (http://www.cbs.dtu.dk/ 25 °C[14]. Virus propagation and purification were per- services/TMHMM-2.0) and the DAS-TM filter server formed as we described previously [17]. RGV genomic (http://mendel.imp.univie.ac.at/sat/DAS)[28]. Repetitive DNA was prepared from purified virus particles. The DNA sequences were detected using REPuter and the purified virus was incubated with TES (10 mM Tris, 1 mM Tandem Repeats Finder [29, 30]. The complete genome EDTA, 1 % SDS, pH 8.0, 100 lg/ml proteinase K) at was scanned for miRNA coding regions using VMir [31], 37 °C for 2 h. Then, the lysate was subjected to phenol- and possible miRNA coding sequences were further ana- chloroform extraction and ethanol precipitation as descri- lyzed using MiPred [32] and RNAfold server (http://rna. bed in our previous work [27]. tbi.univie.ac.at). DNA dot matrix plot analysis was per- Primers were designed based on complete DNA formed using DNAMAN version 6 (Lynnon Corp.). sequence alignments of FV3, tiger frog virus (TFV) and Sequences of 26 core-gene-encoded proteins from 17 STIV, which are shown in Table S2. The amplified PCR other completely sequenced iridoviruses were concatenated products were about 1500 bp in length, and the genes as a continuous amino acid sequence with the same order 123 Genome sequence of Rana grylio virus 1561 Fig. 2 DNA dot plot analysis of the RGV genome in comparison strands of the genome DNA sequences were aligned for the dot matrix with itself and other ranaviruses. The horizontal axis represents the plot. Solid lines show the high level of sequence similarity. Black dots RGV genome. The vertical axes represent (a) the RGV genome, show the results of comparisons of RGV with the positive-sense (b) the FV3 genome, (c) the STIV genome, (d) the TFV genome, strand of the virus indicated in the vertical axis, and red dots show (e) the ATV genome and (f) the EHNV genome. The complete those with the corresponding plus-sense strand. Solid lines show the genomic sequences were aligned using DNAMAN version 6, and both high level of sequence similarity (color figure online) as RGV. LYCIV was not included, as its complete homology to those of other viruses were not annotated in sequence has not been annotated. The phylogenetic tree this work. The locations, sizes, predicted functions and was constructed using MrBayes 3.2 following multi- motifs of each putative ORF are listed in Table S3, together sequence alignment using Clustal X 1.83 and format con- with homologous proteins in other iridoviruses (FV3, version using Mega 4 [33]. A mixed amino acid model STIV, LCDV-C and ISKNV). Eighty-nine percent of the analysis was applied with 100,000 generations and a ORFs have orthologous genes in FV3, 84 % in STIV, and sampling frequency of 100. only 25 % in ISKNV. ORFs were identified by the following criteria [9, 12, A diagrammatic representation of the RGV genome is 34]: (1) they were at least 120 bp long, (2) they could be shown in Fig. 1. Fifty-five ORFs were predicted to have detected by the two annotation methods, and (3) they were functions or functional domains (black arrows) related to not located within larger ORFs or have homologs to at least DNA replication, transcription, nucleotide metabolism, two known virus ORFs. protein synthesis and modification, viral structure, or host- The genome size, G?C content, and potential ORFs of virus interactions (Table S3). Additionally, of the 22 par- RGV were compared to those of other iridoviruses, and tially overlapping ORFs, one (72R) had a corresponding these data are shown in Table S1. The RGV genome ortholog only in the ATV genome, two (38R, 70L) had (GenBank accession no. JQ654586) contained a double- orthologs only in the STIV genome, others had orthologs in stranded DNA consisting of 105,791 bp, with a G?C at least two viruses, and 57R was completely within 56L. content of 55 %. One hundred and six putative ORFs could DNA dot plot analysis comparing the RGV genomic be identified in the RGV genome by computer-assisted DNA with itself and other iridovirus genomes revealed analysis, the length of which ranged from 126 to 3885 bp.
Load more

Recommended publications
  • Identification of Two Major Virion Protein Genes of White Spot Syndrome Virus of Shrimp
    Virology 266, 227–236 (2000) doi:10.1006/viro.1999.0088, 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 Identification of Two Major Virion Protein Genes of White Spot Syndrome Virus of Shrimp Marie¨lle C. W. van Hulten, Marcel Westenberg, Stephen D. Goodall, and Just M. Vlak1 Laboratory of Virology, Wageningen Agricultural University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands Received August 25, 1999; returned to author for revision October 28, 1999; accepted November 8, 1999 White Spot Syndrome Virus (WSSV) is an invertebrate virus, causing considerable mortality in shrimp. Two structural proteins of WSSV were identified. WSSV virions are enveloped nucleocapsids with a bacilliform morphology with an approximate size of 275 ϫ 120 nm, and a tail-like extension at one end. The double-stranded viral DNA has an approximate size 290 kb. WSSV virions, isolated from infected shrimps, contained four major proteins: 28 kDa (VP28), 26 kDa (VP26), 24 kDa (VP24), and 19 kDa (VP19) in size, respectively. VP26 and VP24 were found associated with nucleocapsids; the others were associated with the envelope. N-terminal amino acid sequences of nucleocapsid protein VP26 and the envelope protein VP28 were obtained by protein sequencing and used to identify the respective genes (vp26 and vp28) in the WSSV genome. To confirm that the open reading frames of WSSV vp26 (612) and vp28 (612) are coding for the putative major virion proteins, they were expressed in insect cells using baculovirus vectors and analyzed by Western analysis.
    [Show full text]
  • Artemia Spp., a Susceptible Host and Vector for Lymphocystis Disease Virus
    viruses Article Artemia spp., a Susceptible Host and Vector for Lymphocystis Disease Virus Estefania J. Valverde, Alejandro M. Labella, Juan J. Borrego and Dolores Castro * Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29017 Málaga, Spain; [email protected] (E.J.V.); [email protected] (A.M.L.); [email protected] (J.J.B.) * Correspondence: [email protected]; Tel.: +34-952134214 Received: 8 May 2019; Accepted: 30 May 2019; Published: 1 June 2019 Abstract: Different developmental stages of Artemia spp. (metanauplii, juveniles and adults) were bath-challenged with two isolates of the Lymphocystis disease virus (LCDV), namely, LCDV SA25 (belonging to the species Lymphocystis disease virus 3) and ATCC VR-342 (an unclassified member of the genus Lymphocystivirus). Viral quantification and gene expression were analyzed by qPCR at different times post-inoculation (pi). In addition, infectious titres were determined at 8 dpi by integrated cell culture (ICC)-RT-PCR, an assay that detects viral mRNA in inoculated cell cultures. In LCDV-challenged Artemia, the viral load increased by 2–3 orders of magnitude (depending on developmental stage and viral isolate) during the first 8–12 dpi, with viral titres up to 2.3 102 × Most Probable Number of Infectious Units (MPNIU)/mg. Viral transcripts were detected in the infected Artemia, relative expression values showed a similar temporal evolution in the different experimental groups. Moreover, gilthead seabream (Sparus aurata) fingerlings were challenged by feeding on LCDV-infected metanauplii. Although no Lymphocystis symptoms were observed in the fish, the number of viral DNA copies was significantly higher at the end of the experimental trial and major capsid protein (mcp) gene expression was consistently detected.
    [Show full text]
  • A Herpetofaunal Survey of the Santee National Wildlife Refuge Submitted
    A Herpetofaunal Survey of the Santee National Wildlife Refuge Submitted to the U.S. Fish and Wildlife Service October 5, 2012 Prepared by: Stephen H. Bennett Wade Kalinowsky South Carolina Department of Natural Resources Introduction The lack of baseline inventory data of herpetofauna on the Santee National Wildlife Refuge, in general and the Dingle Pond Unit specifically has proven problematic in trying to assess priority species of concern and direct overall management needs in this system. Dingle Pond is a Carolina Bay which potentially provides unique habitat for many priority reptiles and amphibians including the federally threatened flatwoods salamander, the state endangered gopher frog, state threatened dwarf siren and spotted turtle and several species of conservation concern including the tiger salamander, upland chorus frog (coastal plain populations only), northern cricket frog (coastal plain populations only), many-lined salamander, glossy crayfish snake and black swamp snake. The presence or abundance of these and other priority species in this large Carolina Bay is not known. This project will provide for funds for South Carolina DNR to conduct baseline surveys to census and assess the status of the herpetofauna in and adjacent to the Dingle Pond Carolina Bay. Surveys will involve a variety of sampling techniques including funnel traps, hoop traps, cover boards, netting and call count surveys to identify herpetofauna diversity and abundance. Herpetofauna are particularly vulnerable to habitat changes including climate change and human development activities. Many unique species are endemic to Carolina Bays, a priority habitat that has been greatly diminished across the coastal plain of South Carolina. These species can serve as indicator species of habitat quality and climate changes and baseline data is critical at both the local and regional level.
    [Show full text]
  • Changes to Virus Taxonomy 2004
    Arch Virol (2005) 150: 189–198 DOI 10.1007/s00705-004-0429-1 Changes to virus taxonomy 2004 M. A. Mayo (ICTV Secretary) Scottish Crop Research Institute, Invergowrie, Dundee, U.K. Received July 30, 2004; accepted September 25, 2004 Published online November 10, 2004 c Springer-Verlag 2004 This note presents a compilation of recent changes to virus taxonomy decided by voting by the ICTV membership following recommendations from the ICTV Executive Committee. The changes are presented in the Table as decisions promoted by the Subcommittees of the EC and are grouped according to the major hosts of the viruses involved. These new taxa will be presented in more detail in the 8th ICTV Report scheduled to be published near the end of 2004 (Fauquet et al., 2004). Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (eds) (2004). Virus Taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp. 1258. Recent changes to virus taxonomy Viruses of vertebrates Family Arenaviridae • Designate Cupixi virus as a species in the genus Arenavirus • Designate Bear Canyon virus as a species in the genus Arenavirus • Designate Allpahuayo virus as a species in the genus Arenavirus Family Birnaviridae • Assign Blotched snakehead virus as an unassigned species in family Birnaviridae Family Circoviridae • Create a new genus (Anellovirus) with Torque teno virus as type species Family Coronaviridae • Recognize a new species Severe acute respiratory syndrome coronavirus in the genus Coro- navirus, family Coronaviridae, order Nidovirales
    [Show full text]
  • United States Patent (19) 11 Patent Number: 5,030,200 Judy Et Al
    United States Patent (19) 11 Patent Number: 5,030,200 Judy et al. (45) Date of Patent: "Jul. 9, 1991 54 METHOD FOR ERADICATING INFECTIOUS 4,708,715 11/1987 Troutner et al. ....................... 604/6 BIOLOGICAL CONTAMINANTS IN BODY 4,878,891 1 1/1989 Judy et al. .............................. 604/5 TISSUES Primary Examiner-Stephen C. Pellegrino (75) Inventors: Millard M. Judy; James L. Matthews; Assistant Examiner-Michael Rafa Joseph T. Newman; Franklin Attorney, Agent, or Firm-Johnson & Gibbs Sogandares-Bernal, all of Dallas, Tex. (57) ABSTRACT (73) Assignee: Baylor Research Foundation, Dallas, A method for externally eradicating infectious patho Tex. genic contaminants, such as enveloped viruses, bacteria, * Notice: The portion of the term of this patent trypanosomal and malarial parasites, present in body subsequent to Nov. 7, 2006 has been tissues, such as blood, blood components, semen, skin, disclaimed. and cornea, before the treated body tissues are intro 21) Appl. No.: 433,024 duced into, or transplanted onto, the body of a human or an animal. Such method includes the steps of: (1) 22) Filed: Nov. 6, 1989 admixing an effective, non-toxic amount of photoactive compound, which has a selectively for binding to the Related U.S. Application Data infectious pathogenic biological contaminants present (63) Continuation-in-part of Ser. No. 67,237, Jun. 25, 1987, therein, with the body tissues outside the body to pro Pat. No. 4,878,891. duce resulting body tissues; (2) maintaining the resulting 51 Int. Cl.............................................. A61M 37/00 body tissues in a suitable container in which there is no (52) U.S.
    [Show full text]
  • Viral Diversity in Oral Cavity from Sapajus Nigritus by Metagenomic Analyses
    Brazilian Journal of Microbiology (2020) 51:1941–1951 https://doi.org/10.1007/s42770-020-00350-w ENVIRONMENTAL MICROBIOLOGY - RESEARCH PAPER Viral diversity in oral cavity from Sapajus nigritus by metagenomic analyses Raissa Nunes dos Santos1,2 & Fabricio Souza Campos2,3 & Fernando Finoketti1,2 & Anne Caroline dos Santos1,2 & Aline Alves Scarpellini Campos1,2,3 & Paulo Guilherme Carniel Wagner2,4 & Paulo Michel Roehe 1,2 & Helena Beatriz de Carvalho Ruthner Batista2,5 & Ana Claudia Franco1,2 Received: 20 January 2020 /Accepted: 25 July 2020 / Published online: 11 August 2020 # Sociedade Brasileira de Microbiologia 2020 Abstract Sapajus nigritus are non-human primates which are widespread in South America. They are omnivores and live in troops of up to 40 individuals. The oral cavity is one of the main entry routes for microorganisms, including viruses. Our study proposed the identification of viral sequences from oral swabs collected in a group of capuchin monkeys (n = 5) living in a public park in a fragment of Mata Atlantica in South Brazil. Samples were submitted to nucleic acid extraction and enrichment, which was followed by the construction of libraries. After high-throughput sequencing and contig assembly, we used a pipeline to identify 11 viral families, which are Herpesviridae, Parvoviridae, Papillomaviridae, Polyomaviridae, Caulimoviridae, Iridoviridae, Astroviridae, Poxviridae,andBaculoviridae, in addition to two complete viral genomes of Anelloviridae and Genomoviridae. Some of these viruses were closely related to known viruses, while other fragments are more distantly related, with 50% of identity or less to the currently available virus sequences in databases. In addition to host-related viruses, insect and small vertebrate-related viruses were also found, as well as plant-related viruses, bringing insights about their diet.
    [Show full text]
  • Biochemical and Structural Characterisation of Membrane-Containing Icosahedral Dsdna Bacteriophages Infecting Thermophilic Thermus Thermophilus
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Virology 379 (2008) 10–19 Contents lists available at ScienceDirect Virology journal homepage: www.elsevier.com/locate/yviro Biochemical and structural characterisation of membrane-containing icosahedral dsDNA bacteriophages infecting thermophilic Thermus thermophilus S.T. Jaatinen, L.J. Happonen, P. Laurinmäki, S.J. Butcher, D.H. Bamford ⁎ Department of Biological and Environmental Sciences and Institute of Biotechnology, Biocenter 2, FIN-00014, University of Helsinki, Finland ARTICLE INFO ABSTRACT Article history: Icosahedral dsDNA viruses isolated from hot springs and proposed to belong to the Tectiviridae family infect Received 1 February 2008 the Gram-negative thermophilic Thermus thermophilus bacterium. Seven such viruses were obtained from Returned to author for revision11 March 2008 the Promega Corporation collection. The structural protein patterns of three of these viruses, growing to a Accepted 8 June 2008 high titer, appeared very similar but not identical. The most stable virus, P23-77, was chosen for more Available online 25 July 2008 detailed studies. Analysis of highly purified P23-77 by thin layer chromatography for neutral lipids showed Keywords: lipid association with the virion. Cryo-EM based three-dimensional image reconstruction of P23-77 to 1.4 nm P23-77 resolution revealed an icosahedrally-ordered protein coat, with spikes on the vertices, and an internal P23-72 membrane. The capsid architecture of P23-77 is most similar to that of the archaeal virus SH1. These findings P23-65H further complicate the grouping of icosahedrally-symmetric viruses containing an inner membrane.
    [Show full text]
  • Wildlife Habitat Plan
    WILDLIFE HABITAT PLAN City of Novi, Michigan A QUALITY OF LIFE FOR THE 21ST CENTURY WILDLIFE HABITAT PLAN City of Novi, Michigan A QUALIlY OF LIFE FOR THE 21ST CENTURY JUNE 1993 Prepared By: Wildlife Management Services Brandon M. Rogers and Associates, P.C. JCK & Associates, Inc. ii ACKNOWLEDGEMENTS City Council Matthew C. Ouinn, Mayor Hugh C. Crawford, Mayor ProTem Nancy C. Cassis Carol A. Mason Tim Pope Robert D. Schmid Joseph G. Toth Planning Commission Kathleen S. McLallen, * Chairman John P. Balagna, Vice Chairman lodia Richards, Secretary Richard J. Clark Glen Bonaventura Laura J. lorenzo* Robert Mitzel* Timothy Gilberg Robert Taub City Manager Edward F. Kriewall Director of Planning and Community Development James R. Wahl Planning Consultant Team Wildlife Management Services - 640 Starkweather Plymouth, MI. 48170 Kevin Clark, Urban Wildlife Specialist Adrienne Kral, Wildlife Biologist Ashley long, Field Research Assistant Brandon M. Rogers and Associates, P.C. - 20490 Harper Ave. Harper Woods, MI. 48225 Unda C. lemke, RlA, ASLA JCK & Associates, Inc. - 45650 Grand River Ave. Novi, MI. 48374 Susan Tepatti, Water Resources Specialist * Participated with the Planning Consultant Team in developing the study. iii TABLE OF CONTENTS ACKNOWLEDGEMENTS iii PREFACE vii EXECUTIVE SUMMARY viii FRAGMENTATION OF NATURAL RESOURCES " ., , 1 Consequences ............................................ .. 1 Effects Of Forest Fragmentation 2 Edges 2 Reduction of habitat 2 SPECIES SAMPLING TECHNIQUES ................................ .. 3 Methodology 3 Survey Targets ............................................ ., 6 Ranking System ., , 7 Core Reserves . .. 7 Wildlife Movement Corridor .............................. .. 9 FIELD SURVEY RESULTS AND RECOMMENDATIONS , 9 Analysis Results ................................ .. 9 Core Reserves . .. 9 Findings and Recommendations , 9 WALLED LAKE CORE RESERVE - DETAILED STUDy.... .. .... .. .... .. 19 Results and Recommendations ............................... .. 21 GUIDELINES TO ECOLOGICAL LANDSCAPE PLANNING AND WILDLIFE CONSERVATION.
    [Show full text]
  • A Novel Family of Large Cationic Proteins That Condense Viral Genomic DNA for Encapsidation
    biology Communication Ascovirus P64 Homologs: A Novel Family of Large Cationic Proteins That Condense Viral Genomic DNA for Encapsidation Dennis K. Bideshi 1,2,* , Tatsinda Spears 3, Heba A. H. Zaghloul 3, Yeping Tan 2, Yves Bigot 4 and Brian A. Federici 2,3 1 Department of Biological Sciences, California Baptist University, Magnolia Avenue, Riverside, CA 92504, USA 2 Department of Entomology, University of California, Riverside, CA 92521, USA; [email protected] (Y.T.); [email protected] (B.A.F.) 3 Graduate Program in Cell, Molecular and Developmental Biology, and Microbiology, University of California, Riverside, CA 92521, USA; [email protected] (T.S.); [email protected] (H.A.H.Z.) 4 UMR CNRS7247, Centre INRA Val de Loire, 37380 Nouzilly, France; [email protected] * Correspondence: [email protected]; Tel.: +1-951-343-4397 Received: 9 August 2018; Accepted: 7 September 2018; Published: 11 September 2018 Abstract: Eukaryotic dsDNA viruses use small basic protamine-like proteins or histones, typically <15 kDa, to condense and encapsidate their genomic (g)DNAs during virogenesis. Ascoviruses are large dsDNA (~100–200 kbp) viruses that are pathogenic to lepidopteran larvae. Little is known about the molecular basis for condensation and encapsidation of their gDNAs. Previous proteomic analysis showed that Spodoptera frugiperda ascovirus (SfAV-1a) virions contain a large unique DNA-binding protein (P64; 64 kDa, pI = 12.2) with a novel architecture proposed to condense its gDNA. Here we used physical, biochemical, and transmission electron microscopy techniques to demonstrate that P64’s basic C-terminal domain condenses SfAV-1a gDNA. Moreover, we demonstrate that only P64 homologs in other ascovirus virions are unique in stably binding DNA.
    [Show full text]
  • The DNA Virus Invertebrate Iridescent Virus 6 Is a Target of the Drosophila Rnai Machinery
    The DNA virus Invertebrate iridescent virus 6 is a target of the Drosophila RNAi machinery Alfred W. Bronkhorsta,1, Koen W. R. van Cleefa,1, Nicolas Vodovarb,2, Ikbal_ Agah Ince_ c,d,e, Hervé Blancb, Just M. Vlakc, Maria-Carla Salehb,3, and Ronald P. van Rija,3 aDepartment of Medical Microbiology, Nijmegen Centre for Molecular Life Sciences, Nijmegen Institute for Infection, Inflammation, and Immunity, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands; bViruses and RNA Interference Group, Institut Pasteur, Centre National de la Recherche Scientifique, Unité de Recherche Associée 3015, 75015 Paris, France; cLaboratory of Virology, Wageningen University, 6708 PB Wageningen, The Netherlands; dDepartment of Genetics and Bioengineering, Yeditepe University, Istanbul 34755, Turkey; and eDepartment of Biosystems Engineering, Faculty of Engineering, Giresun University, Giresun 28100, Turkey Edited by Peter Palese, Mount Sinai School of Medicine, New York, NY, and approved October 19, 2012 (received for review April 28, 2012) RNA viruses in insects are targets of an RNA interference (RNAi)- sequently, are hypersensitive to virus infection and succumb more based antiviral immune response, in which viral replication inter- rapidly than their wild-type (WT) controls (11–14). mediates or viral dsRNA genomes are processed by Dicer-2 (Dcr-2) Small RNA cloning and next-generation sequencing provide into viral small interfering RNAs (vsiRNAs). Whether dsDNA virus detailed insights into vsiRNA biogenesis. In several studies in infections are controlled by the RNAi pathway remains to be insects, the polarity of the vsiRNA population deviates strongly determined. Here, we analyzed the role of RNAi in DNA virus from the highly skewed distribution of positive strand (+) over infection using Drosophila melanogaster infected with Invertebrate negative (−) viral RNAs that is generally observed in (+) RNA iridescent virus 6 (IIV-6) as a model.
    [Show full text]
  • Ecology and Pathology of Amphibian Ranaviruses
    Vol. 87: 243–266, 2009 DISEASES OF AQUATIC ORGANISMS Published December 3 doi: 10.3354/dao02138 Dis Aquat Org OPENPEN ACCESSCCESS REVIEW Ecology and pathology of amphibian ranaviruses Matthew J. Gray1,*, Debra L. Miller1, 2, Jason T. Hoverman1 1274 Ellington Plant Sciences Building, Center for Wildlife Health, Department of Forestry Wildlife and Fisheries, Institute of Agriculture, University of Tennessee, Knoxville, Tennessee 37996-4563, USA 2Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, 43 Brighton Road, Tifton, Georgia 31793, USA ABSTRACT: Mass mortality of amphibians has occurred globally since at least the early 1990s from viral pathogens that are members of the genus Ranavirus, family Iridoviridae. The pathogen infects multiple amphibian hosts, larval and adult cohorts, and may persist in herpetofaunal and oste- ichthyan reservoirs. Environmental persistence of ranavirus virions outside a host may be several weeks or longer in aquatic systems. Transmission occurs by indirect and direct routes, and includes exposure to contaminated water or soil, casual or direct contact with infected individuals, and inges- tion of infected tissue during predation, cannibalism, or necrophagy. Some gross lesions include swelling of the limbs or body, erythema, swollen friable livers, and hemorrhage. Susceptible amphi- bians usually die from chronic cell death in multiple organs, which can occur within a few days fol- lowing infection or may take several weeks. Amphibian species differ in their susceptibility to rana- viruses, which may be related to their co-evolutionary history with the pathogen. The occurrence of recent widespread amphibian population die-offs from ranaviruses may be an interaction of sup- pressed and naïve host immunity, anthropogenic stressors, and novel strain introduction.
    [Show full text]
  • Viruses in a 14Th-Century Coprolite
    AEM Accepts, published online ahead of print on 7 February 2014 Appl. Environ. Microbiol. doi:10.1128/AEM.03242-13 Copyright © 2014, American Society for Microbiology. All Rights Reserved. 1 Title: Viruses in a 14th-century coprolite 2 Running title: Viruses in a 14th-century coprolite 3 4 Sandra Appelt1,*, Laura Fancello1,*, Matthieu Le Bailly2, Didier Raoult1, Michel Drancourt1, 5 Christelle Desnues†,1 6 7 1 Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13385 8 Marseille, France. 9 2 Franche-Comté University, CNRS UMR 6249 Chrono-Environment, 25 030 Besançon, France. 10 * These authors have contributed equally to this work 11 † Corresponding author: 12 Christelle Desnues, Unité de recherche sur les maladies infectieuses et tropicales émergentes 13 (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Faculté de médecine, Aix Marseille 14 Université, 27 Bd Jean Moulin, 13385 Marseille, France. Tel: (+33) 4 91 38 46 30, Fax: (+33) 4 15 91 38 77 72. 16 Email: [email protected] 17 Number of words in Abstract: 133 words 18 Number of words in Main Text: 2538 words 19 Number of words in Methods: 954 words 20 Figures: 4, Supplementary Figures: 3 21 Tables: 0, Supplementary Tables: 6 22 Keywords: coprolite, paleomicrobiology, metagenomics, bacteriophages, viruses, ancient DNA 1 23 Abstract 24 Coprolites are fossilized fecal material that can reveal information about ancient intestinal and 25 environmental microbiota. Viral metagenomics has allowed systematic characterization of viral 26 diversity in environmental and human-associated specimens, but little is known about the viral 27 diversity in fossil remains. Here, we analyzed the viral community of a 14th-century coprolite 28 from a closed barrel in a Middle Age site in Belgium using electron microscopy and 29 metagenomics.
    [Show full text]