1887

Abstract

Betanodaviruses have bi-segmented positive-sense RNA genomes, consisting of RNAs 1 and 2. For some members of the related genus alphanodavirus, the 3′ terminal 50 nucleotides (nt) of RNA2, including a predicted stem-loop structure (3′SL), are essential for replication. We investigate the possible existence and role of a similar structure in a reassortant betanodavirus strain (RGNNV/SJNNV). In this study, we developed three recombinant strains containing nucleotide changes at positions 1408 and 1412. Predictive models showed stem-loop structures involving nt 1398–1421 of the natural reassortant whereas this structure is modified in the recombinant viruses harbouring point mutations r1408 and r1408–1412, but not in r1412. Results obtained from infectivity assays showed differences between the reference strains and the mutants in both RNA1 and RNA2 synthesis. Moreover, an imbalance between the synthesis of both segments was demonstrated, mainly with the double mutant. All these results suggest an interaction between RNA1 and the 3′ non-coding regions (3′NCR) of RNA2. In addition, the significant attenuation of the virulence for Senegalese sole and the delayed replication of r1408–1412 in brain tissues may point to an interaction of RNA2 with host cellular proteins.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001112
2018-07-24
2019-10-17
Loading full text...

Full text loading...

/deliver/fulltext/jgv/99/9/1210.html?itemId=/content/journal/jgv/10.1099/jgv.0.001112&mimeType=html&fmt=ahah

References

  1. Thiéry R, Johnson KL, Nakai T, Schneemann A, Bonami JR et al. FamilyNodaviridae. In King AMQ, Adams MJ, Lefkowitz EJ. (editors) Ninth Report of the International Committee on Taxonomy of Viruses San Diego, CA, USA: Elsevier Academic Press; 2011; pp.1061–1067
    [Google Scholar]
  2. Iwamoto T, Mise K, Takeda A, Okinaka Y, Mori K et al. Characterization of striped jack nervous necrosis virus subgenomic RNA3 and biological activities of its encoded protein B2. J Gen Virol 2005;86:2807–2816 [CrossRef][PubMed]
    [Google Scholar]
  3. Chen LJ, Su YC, Hong JR. Betanodavirus non-structural protein B1: a novel anti-necrotic death factor that modulates cell death in early replication cycle in fish cells. Virology 2009;385:444–454 [CrossRef][PubMed]
    [Google Scholar]
  4. Nishizawa T, Furuhashi M, Nagai T, Nakai T, Muroga K. Genomic classification of fish nodaviruses by molecular phylogenetic analysis of the coat protein gene. Appl Environ Microbiol 1997;63:1633–1636[PubMed]
    [Google Scholar]
  5. Olveira JG, Souto S, Dopazo CP, Thiéry R, Barja JL et al. Comparative analysis of both genomic segments of betanodaviruses isolated from epizootic outbreaks in farmed fish species provides evidence for genetic reassortment. J Gen Virol 2009;90:2940–2951 [CrossRef][PubMed]
    [Google Scholar]
  6. Panzarin V, Fusaro A, Monne I, Cappellozza E, Patarnello P et al. Molecular epidemiology and evolutionary dynamics of betanodavirus in southern Europe. Infect Genet Evol 2012;12:63–70 [CrossRef][PubMed]
    [Google Scholar]
  7. Toffolo V, Negrisolo E, Maltese C, Bovo G, Belvedere P et al. Phylogeny of betanodaviruses and molecular evolution of their RNA polymerase and coat proteins. Mol Phylogenet Evol 2007;43:298–308 [CrossRef][PubMed]
    [Google Scholar]
  8. Souto S, Mérour E, Biacchesi S, Brémont M, Olveira JG et al. In vitro and in vivo characterization of molecular determinants of virulence in reassortant betanodavirus. J Gen Virol 2015;96:1287–1296 [CrossRef][PubMed]
    [Google Scholar]
  9. Toffan A, Pascoli F, Pretto T, Panzarin V, Abbadi M et al. Viral nervous necrosis in gilthead sea bream (Sparus aurata) caused by reassortant betanodavirus RGNNV/SJNNV: an emerging threat for Mediterranean aquaculture. Sci Rep 2017;7:46755 [CrossRef][PubMed]
    [Google Scholar]
  10. Ahlquist P. RNA-dependent RNA polymerases, viruses, and RNA silencing. Science 2002;296:1270–1273 [CrossRef][PubMed]
    [Google Scholar]
  11. Gerber K, Wimmer E, Paul AV. Biochemical and genetic studies of the initiation of human rhinovirus 2 RNA replication: identification of a cis-replicating element in the coding sequence of 2A(pro). J Virol 2001;75:10979–10990 [CrossRef][PubMed]
    [Google Scholar]
  12. Goodfellow I, Chaudhry Y, Richardson A, Meredith J, Almond JW et al. Identification of a cis-acting replication element within the poliovirus coding region. J Virol 2000;74:4590–4600 [CrossRef][PubMed]
    [Google Scholar]
  13. Panaviene Z, Panavas T, Nagy PD. Role of an internal and two 3'-terminal RNA elements in assembly of tombusvirus replicase. J Virol 2005;79:10608–10618 [CrossRef][PubMed]
    [Google Scholar]
  14. Park JW, Desvoyes B, Scholthof HB. Tomato bushy stunt virus genomic RNA accumulation is regulated by interdependent cis-acting elements within the movement protein open reading frames. J Virol 2002;76:12747–12757 [CrossRef][PubMed]
    [Google Scholar]
  15. Tatsuta M, Mizumoto H, Kaido M, Mise K, Okuno T. The red clover necrotic mosaic virus RNA2 trans-activator is also a cis-acting RNA2 replication element. J Virol 2005;79:978–986 [CrossRef][PubMed]
    [Google Scholar]
  16. Wu B, Pogany J, Na H, Nicholson BL, Nagy PD et al. A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA-based regulation of viral processes. PLoS Pathog 2009;5:e1000323 [CrossRef][PubMed]
    [Google Scholar]
  17. Nagashima S, Sasaki J, Taniguchi K. The 5'-terminal region of the Aichi virus genome encodes cis-acting replication elements required for positive- and negative-strand RNA synthesis. J Virol 2005;79:6918–6931 [CrossRef][PubMed]
    [Google Scholar]
  18. Sun X, Simon AE. A cis-replication element functions in both orientations to enhance replication of Turnip crinkle virus. Virology 2006;352:39–51 [CrossRef][PubMed]
    [Google Scholar]
  19. Albariño CG, Eckerle LD, Ball LA. The cis-acting replication signal at the 3' end of Flock House virus RNA2 is RNA3-dependent. Virology 2003;311:181–191 [CrossRef][PubMed]
    [Google Scholar]
  20. Ball LA. Nodavirus. In Webster RG, Granoff A. (editors) Encyclopaedia of Virology London, UK: Academic Press Limited; 1994; pp.919–925
    [Google Scholar]
  21. Ball LA, Li Y. cis-acting requirements for the replication of flock house virus RNA 2. J Virol 1993;67:3544–3551[PubMed]
    [Google Scholar]
  22. Li Y, Ball LA. Nonhomologous RNA recombination during negative-strand synthesis of flock house virus RNA. J Virol 1993;67:3854–3860[PubMed]
    [Google Scholar]
  23. Lindenbach BD, Sgro JY, Ahlquist P. Long-distance base pairing in flock house virus RNA1 regulates subgenomic RNA3 synthesis and RNA2 replication. J Virol 2002;76:3905–3919 [CrossRef][PubMed]
    [Google Scholar]
  24. Rosskopf JJ, Upton JH, Rodarte L, Romero TA, Leung MY et al. A 3' terminal stem-loop structure in Nodamura virus RNA2 forms an essential cis-acting signal for RNA replication. Virus Res 2010;150:12–21 [CrossRef][PubMed]
    [Google Scholar]
  25. Taufer M, Leung MY, Solorio T, Licon A, Mireles D et al. RNAVLab: a virtual laboratory for studying RNA secondary structures based on grid computing technology. Parallel Comput 2008;34:661–680 [CrossRef][PubMed]
    [Google Scholar]
  26. An M, Iwakawa HO, Mine A, Kaido M, Mise K et al. A Y-shaped RNA structure in the 3' untranslated region together with the trans-activator and core promoter of Red clover necrotic mosaic virus RNA2 is required for its negative-strand RNA synthesis. Virology 2010;405:100–109 [CrossRef][PubMed]
    [Google Scholar]
  27. Dreher TW. Functions of the 3'-untranslated regions of positive strand RNA viral genomes. Annu Rev Phytopathol 1999;37:151–174 [CrossRef][PubMed]
    [Google Scholar]
  28. Proutski V, Gritsun TS, Gould EA, Holmes EC. Biological consequences of deletions within the 3'-untranslated region of flaviviruses may be due to rearrangements of RNA secondary structure. Virus Res 1999;64:107–123 [CrossRef][PubMed]
    [Google Scholar]
  29. Sáiz M, Gómez S, Martínez-Salas E, Sobrino F. Deletion or substitution of the aphthovirus 3' NCR abrogates infectivity and virus replication. J Gen Virol 2001;82:93–101 [CrossRef][PubMed]
    [Google Scholar]
  30. Zhong W, Rueckert RR. Flock house virus: down-regulation of subgenomic RNA3 synthesis does not involve coat protein and is targeted to synthesis of its positive strand. J Virol 1993;67:2716–2722[PubMed]
    [Google Scholar]
  31. Gallagher TM, Friesen PD, Rueckert RR. Autonomous replication and expression of RNA 1 from black beetle virus. J Virol 1983;46:481–789[PubMed]
    [Google Scholar]
  32. Eckerle LD, Ball LA. Replication of the RNA segments of a bipartite viral genome is coordinated by a transactivating subgenomic RNA. Virology 2002;296:165–176 [CrossRef][PubMed]
    [Google Scholar]
  33. Eckerle LD, Albariño CG, Ball LA. Flock House virus subgenomic RNA3 is replicated and its replication correlates with transactivation of RNA2. Virology 2003;317:95–108 [CrossRef][PubMed]
    [Google Scholar]
  34. Chen CJ, Kuo MD, Chien LJ, Hsu SL, Wang YM et al. RNA-protein interactions: involvement of NS3, NS5, and 3' noncoding regions of Japanese encephalitis virus genomic RNA. J Virol 1997;71:3466–3473[PubMed]
    [Google Scholar]
  35. Ta M, Vrati S. Mov34 protein from mouse brain interacts with the 3' noncoding region of Japanese encephalitis virus. J Virol 2000;74:5108–5115 [CrossRef][PubMed]
    [Google Scholar]
  36. Vashist S, Anantpadma M, Sharma H, Vrati S. La protein binds the predicted loop structures in the 3' non-coding region of Japanese encephalitis virus genome: role in virus replication. J Gen Virol 2009;90:1343–1352 [CrossRef][PubMed]
    [Google Scholar]
  37. de Nova-Ocampo M, Villegas-Sepúlveda N, del Angel RM. Translation elongation factor-1α, La, and PTB interact with the 3' untranslated region of dengue 4 virus RNA. Virology 2002;295:337–347 [CrossRef][PubMed]
    [Google Scholar]
  38. García-Montalvo BM, Medina F, del Angel RM. La protein binds to NS5 and NS3 and to the 5' and 3' ends of Dengue 4 virus RNA. Virus Res 2004;102:141–150 [CrossRef][PubMed]
    [Google Scholar]
  39. Ito T, Lai MM. Determination of the secondary structure of and cellular protein binding to the 3'-untranslated region of the hepatitis C virus RNA genome. J Virol 1997;71:8698–8706[PubMed]
    [Google Scholar]
  40. Gutiérrez-Escolano AL, Vázquez-Ochoa M, Escobar-Herrera J, Hernández-Acosta J. La, PTB, and PAB proteins bind to the 3' untranslated region of Norwalk virus genomic RNA. Biochem Biophys Res Commun 2003;311:759–766 [CrossRef][PubMed]
    [Google Scholar]
  41. Seganti L, Superti F, Bianchi S, Orsi N, Divizia M et al. Susceptibility of mammalian, avian, fish, and mosquito cell lines to rabies virus infection. Acta Virol 1990;34:155–163[PubMed]
    [Google Scholar]
  42. Frerichs GN, Rodger HD, Peric Z. Cell culture isolation of piscine neuropathy nodavirus from juvenile sea bass, Dicentrarchus labrax. J Gen Virol 1996;77:2067–2071 [CrossRef][PubMed]
    [Google Scholar]
  43. Iwamoto T, Nakai T, Mori K, Arimoto M, Furusawa I. Cloning of the fish cell line SSN-1 for piscine nodaviruses. Dis Aquat Organ 2000;43:81–89 [CrossRef][PubMed]
    [Google Scholar]
  44. Reed LJ, Müench H. A simple method of estimating fifty per cent endpoints. Am J Epidemiol 1938;27:493–497 [CrossRef]
    [Google Scholar]
  45. Buchholz UJ, Finke S, Conzelmann KK. Generation of bovine respiratory syncytial virus (BRSV) from cDNA: BRSV NS2 is not essential for virus replication in tissue culture, and the human RSV leader region acts as a functional BRSV genome promoter. J Virol 1999;73:251–259[PubMed]
    [Google Scholar]
  46. Andronescu MS, Pop C, Condon AE. Improved free energy parameters for RNA pseudoknotted secondary structure prediction. RNA 2010;16:26–42 [CrossRef][PubMed]
    [Google Scholar]
  47. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003;31:3406–3415 [CrossRef][PubMed]
    [Google Scholar]
  48. Olveira JG, Souto S, Dopazo CP, Bandín I. Isolation of betanodavirus from farmed turbot Psetta maxima showing no signs of viral encephalopathy and retinopathy. Aquaculture 2013;406-407:125–130 [CrossRef]
    [Google Scholar]
  49. Purcell MK, Hart SA, Kurath G, Winton JR. Strand-specific, real-time RT-PCR assays for quantification of genomic and positive-sense RNAs of the fish rhabdovirus, Infectious hematopoietic necrosis virus. J Virol Methods 2006;132:18–24 [CrossRef][PubMed]
    [Google Scholar]
  50. Nishizawa T, Mori K, Nakai T, Furusawa I, Muroga K. Polymerase chain reaction (PCR) amplification of RNA of striped jack nervous necrosis virus (SJNNV). Dis Aquat Organ 1994;18:103–107 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.001112
Loading
/content/journal/jgv/10.1099/jgv.0.001112
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error