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Volume 83, Issue 4

Shrimp Taura syndrome virus: genomic characterization and similarity with members of the genus Free

Abstract

The single-stranded genomic RNA of Taura syndrome virus (TSV) is 10205 nucleotides in length, excluding the 3′ poly(A) tail, and contains two large open reading frames (ORFs) that are separated by an intergenic region of 207 nucleotides. The ORFs are flanked by a 377 nucleotide 5′ untranslated region (UTR) and a 226 nucleotide 3′ UTR followed by a poly(A) tail. The predicted amino acid sequence of ORF1 revealed sequence motifs characteristic of a helicase, a protease and an RNA-dependent RNA polymerase, similar to the non-structural proteins of several plant and animal RNA viruses. In addition, a short amino acid sequence located in the N-terminal region of ORF1 presented a significant similarity with a baculovirus IAP repeat (BIR) domain of inhibitor of apoptosis proteins from double-stranded DNA viruses and from animals. The presence of this BIR-like sequence is the first reported in a single-stranded RNA virus, but its function is unknown. The N-terminal amino acid sequence of three TSV capsid proteins (55, 40 and 24 kDa) were mapped in ORF2, which is not in the same reading frame as ORF1 and possesses an AUG codon upstream of the structural genes. However, the intergenic region shows nucleotide sequence similarity with those of the genus , suggesting a similar non-AUG-mediated translation mechanism. The structure of the TSV genome [5′ UTR–non-structural proteins–intergenic UTR–structural proteins–3′ UTR–poly(A) tail] is similar to those of small insect-infecting RNA viruses, which were recently regrouped into a new virus genus, .

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2002-04-01
2024-04-19
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References

  1. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. 1997; Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25:3389–3402
     [Google Scholar]
  2. Bergmann E. M., Mosimann S. C., Chernaia M. M., Malcolm B. A., James M. N. G. 1997; The refined crystal structure of the 3C gene product from hepatitis A virus: specific proteinase activity and RNA recognition. Journal of Virology 71:2436–2448
     [Google Scholar]
  3. Birnbaum M. J., Clem R. J., Miller L. K. 1994; An apoptosis-inhibiting gene from a nuclear polyhedrosis virus encoding a polypeptide with Cys/His sequence motifs. Journal of Virology 68:2521–2528
     [Google Scholar]
  4. Bonami J.-R., Hasson K. W., Mari J., Poulos B. T., Lightner D. V. 1997; Taura syndrome of marine penaeid shrimp: characterization of the viral agent. Journal of General Virology 78:313–319
     [Google Scholar]
  5. Brock J. A., Gose R., Lightner D. V., Hasson K. W. 1995; An overview of Taura syndrome, an important disease of farmed Penaeus vannamei. In Swimming Through Troubled Water. Proceedings of the Special Session on Shrimp Farming pp 84–94 Edited by Browdy C. L., Hopkins J. S. Baton Rouge, LA: World Aquaculture Society;
     [Google Scholar]
  6. Cavener D. R., Ray S. C. 1991; Eukaryotic start and stop translation sites. Nucleic Acids Research 19:3185–3192
     [Google Scholar]
  7. Cohen J. I., Ticehurst J. R., Purcell R. H., Buckler-White A., Baroudy B. M. 1987; Complete nucleotide sequence of wild-type hepatitis A virus: comparison with different strains of hepatitis A virus and other picornaviruses. Journal of Virology 61:50–59
     [Google Scholar]
  8. Crook N. E., Clem R. J., Miller L. K. 1993; An apoptosis-inhibiting baculovirus gene with a zinc finger-like motif. Journal of Virology 67:2168–2174
     [Google Scholar]
  9. Czibener C., La Torre J. L., Muscio O. A., Ugalde R. A., Scodeller E. A. 2000; Nucleotide sequence analysis of Triatoma virus shows that it is a member of a novel group of insect RNA viruses. Journal of General Virology 81:1149–1154
     [Google Scholar]
  10. Deveraux Q. L., Reed J. C. 1999; IAP family proteins: suppressors of apoptosis. Genes & Development 13:239–252
     [Google Scholar]
  11. Doherty M., Todd D., McFerran N., Hoey E. M. 1999; Sequence analysis of a porcine enterovirus serotype 1 isolate: relationships with other picornaviruses. Journal of General Virology 80:1929–1941
     [Google Scholar]
  12. Domier L. L., McCoppin N. K., D’Arcy C. J. 2000; Sequence requirements for translation initiation of Rhopalosiphum padi virus ORF2. Virology 268:264–271
     [Google Scholar]
  13. Felsenstein J. 1993 PHYLIP: Phylogeny Inference Package, version 3·5 University of Washington; Seattle, WA, USA:
     [Google Scholar]
  14. Ghosh R. C., Ball B. V., Willcocks M. M., Carter M. J. 1999; The nucleotide sequence of sacbrood virus of the honey bee: an insect picorna-like virus. Journal of General Virology 80:1541–1549
     [Google Scholar]
  15. Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. 1989a; Two superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acid Research 17:4713–4730
     [Google Scholar]
  16. Gorbalenya A. E., Donchenko A. P., Blinov V. M., Koonin E. V. 1989b; Cysteine proteases of positive strand viruses and chymotrypsin-like serine proteases. A distinct protein superfamily with a common structural fold. FEBS Letters 243:103–114
     [Google Scholar]
  17. Guilford P. J., Beck D. L., Forster R. L. 1991; Influence of the poly(A) tail and putative polyadenylation signal on the infectivity of white clover mosaic potexvirus. Virology 182:61–67
     [Google Scholar]
  18. Harris K. S., Xiang W., Alexander L., Lane W. S., Paul A. V., Wimmer E. 1994; Interaction of poliovirus polypeptide 3CDpro with the 5′ and 3′ termini of the poliovirus genome. Identification of viral and cellular cofactors needed for efficient binding. Journal of Biological Chemistry 269:27004–27014
     [Google Scholar]
  19. Hasson K. W., Lightner D. V., Poulos B. T., Redman R. M., White B. L., Brock J. A., Bonami J.-R. 1995; Taura syndrome in Penaeus vannamei : demonstration of a viral etiology. Diseases of Aquatic Organisms 23:115–126
     [Google Scholar]
  20. Hasson K. W., Lightner D. V., Mari J., Bonami J.-R., Poulos B. T., Mohney L. L., Redman R. M., Brock J. A. 1999; The geographic distribution of Taura syndrome virus (TSV) in the Americas: determination by histopathology and in situ hybridization using TSV-specific cDNA probes. Aquaculture 171:13–26
     [Google Scholar]
  21. Hinds M. G., Norton R. S., Vaux D. L., Day C. L. 1999; Solution structure of a baculoviral inhibitor of apoptosis (IAP) repeat. Nature Structural Biology 6:648–651
     [Google Scholar]
  22. Isawa H., Asano S., Sahara K., Iizuka T., Bando H. 1998; Analysis of genetic information of an insect picorna-like virus, infectious flacherie virus of silkworm: evidence for evolutionary relationships among insect, mammalian and plant picorna(-like) viruses. Archives of Virology 143:127–143
     [Google Scholar]
  23. Johnson K. N., Christian P. D. 1998; The novel genome organization of the insect picorna-like virus Drosophila C virus suggests this virus belongs to a previously undescribed virus family. Journal of General Virology 79:191–203
     [Google Scholar]
  24. Koonin E. V. 1991; The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. Journal of General Virology 72:2197–2206
     [Google Scholar]
  25. Koonin E. V., Dolja V. V. 1993; Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Critical Reviews in Biochemistry and Molecular Biology 28:375–430
     [Google Scholar]
  26. Leat N., Ball B., Govan V., Davison S. 2000; Analysis of the complete genome sequence of black queen-cell virus, a picorna-like virus of honey bees. Journal of General Virology 81:2111–2119
     [Google Scholar]
  27. Li F., Ambrosini G., Chu E. Y., Plescia J., Tognin S., Marchisio P. C., Altieri D. C. 1998; Control of apoptosis and mitotic spindle checkpoint by survivin. Nature 396:580–584
     [Google Scholar]
  28. Li F., Flanary P. L., Altieri D. C., Dohlman H. G. 2000; Cell division regulation by BIR1, a member of the inhibitor of apoptosis in yeast. Journal of Biological Chemistry 275:6707–6711
     [Google Scholar]
  29. Lightner D. V. 1996; Epizootiology, distribution and the impact on international trade of two penaeid shrimp viruses in the Americas. Revue Scientifique et Technique Office International des Epizooties 15:579–601
     [Google Scholar]
  30. Lightner D. V., Redman R. M. 1998; Strategies for the control of viral diseases of shrimp in the Americas. Fish Pathology 33:165–180
     [Google Scholar]
  31. Mari J., Bonami J.-R., Lightner D. V. 1998; Taura syndrome of penaeid shrimp: cloning of viral genome fragments and development of specific gene probes. Diseases of Aquatic Organisms 33:11–17
     [Google Scholar]
  32. Marvil P., Knowles N. J., Mockett A. P. A., Britton P., Brown T. D. K., Cavanagh D. 1999; Avian encephalomyelitis virus is a picornavirus and is most closely related to hepatitis A virus. Journal of General Virology 80:653–662
     [Google Scholar]
  33. Mathews D. H., Sabina J., Zuker M., Turner D. H. 1999; Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of Molecular Biology 288:911–940
     [Google Scholar]
  34. Moon J. S., Domier L. L., McCoppin N. K., D’Arcy C. J., Jin H. 1998; Nucleotide sequence analysis shows that Rhopalosiphum padi virus is a member of a novel group of insect-infecting RNA viruses. Virology 243:54–65
     [Google Scholar]
  35. Nainan O. V., Margolis H. S., Robertson B. H., Balayan M., Brinton M. A. 1991; Sequence analysis of a new hepatitis A virus naturally infecting cynomolgus macaques ( Macaca fascicularis ). Journal of General Virology 72:1685–1689
     [Google Scholar]
  36. Najarian R., Caput D., Gee W., Potter S. J., Renard A., Merryweather J., Van Nest G., Dina D. 1985; Primary structure and gene organization of human hepatitis A virus. Proceedings of the National Academy of Sciences, USA 82:2627–2631
     [Google Scholar]
  37. Nakashima N., Sasaki J., Toriyama S. 1999; Determining the nucleotide sequence and capsid-coding region of Himetobi P virus: a member of a novel group of RNA viruses that infect insects. Archives of Virology 144:2051–2058
     [Google Scholar]
  38. O’Brien V. 1998; Viruses and apoptosis. Journal of General Virology 79:1833–1845
     [Google Scholar]
  39. Overstreet R. M., Lightner D. V., Hasson K. W., McIlwain S., Lotz J. M. 1997; Susceptibility to Taura syndrome virus of some penaeid shrimp species native to the Gulf of Mexico and the Southeastern United States. Journal of Invertebrate Pathology 69:165–176
     [Google Scholar]
  40. Pearson W. R., Lipman D. J. 1988; Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences, USA 85:2444–2448
     [Google Scholar]
  41. Ryan M. D., Flint M. 1997; Virus-encoded proteinases of the picornavirus super-group. Journal of General Virology 78:699–723
     [Google Scholar]
  42. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
  43. Sasaki J., Nakashima N. 1999; Translation initiation at the CUU codon is mediated by the internal ribosome entry site of an insect picorna-like virus in vitro. Journal of Virology 73:1219–1226
     [Google Scholar]
  44. Sasaki J., Nakashima N. 2000; Methionine-independent initiation of translation in the capsid protein of an insect RNA virus. Proceedings of the National Academy of Sciences, USA 97:1512–1515
     [Google Scholar]
  45. Sasaki J., Nakashima N., Saito H., Noda H. 1998; An insect picorna-like virus, Plautia stali intestine virus, has genes of capsid proteins in the 3′ part of the genome. Virology 244:50–58
     [Google Scholar]
  46. Thompson J. D., Higgins D. G., Gibson T. J. 1994; CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment though sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22:4673–4680
     [Google Scholar]
  47. Tsarev S. A., Emerson S. U., Balayan M. S., Ticehurst J., Purcell R. H. 1991; Simian hepatitis A virus (HAV) strain AGM-27: comparison of genome structure and growth in cell culture with other HAV strains. Journal of General Virology 72:1677–1683
     [Google Scholar]
  48. Uren A. G., Beilharz T., O’Connell M. J., Bugg S. J., van Driel R., Vaux D. L., Lithgow T. 1999; Role for yeast inhibitor of apoptosis (IAP)-like proteins in cell division. Proceedings of the National Academy of Sciences, USA 96:10170–10175
     [Google Scholar]
  49. van der Wilk F., Dullemans A. M., Verbeek M., Van den Heuvel J. F. J. M. 1997; Nucleotide sequence and genomic organization of Acyrthosiphon pisum virus. Virology 238:353–362
     [Google Scholar]
  50. van Regenmortel M. H. V., Fauquet C. M., Bishop D. H. L., Cartens E. B., Estes M. K., Lemon S. M., Maniloff J., Mayo M. A., McGeoch D. J., Pringle C. R., Wickner R. B. (editors) 2000; Virus Taxonomy. Seventh Report of the International Committee on Taxonomy of Viruses San Diego: Academic Press;
     [Google Scholar]
  51. Wilson J. E., Powell M. J., Hoover S. E., Sarnow P. 2000a; Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Molecular and Cellular Biology 20:4990–4999
     [Google Scholar]
  52. Wilson J. E., Pestova T. V., Hellen C. U., Sarnow P. 2000b; Initiation of protein synthesis from the A site of the ribosome. Cell 102:511–520
     [Google Scholar]
  53. Yamashita T., Sakae K., Tsuzuki H., Suzuki Y., Ishikawa N., Takeda N., Miyamura T., Yamazaki S. 1998; Complete nucleotide sequence and genetic organization of Aichi virus, a distinct member of the Picornaviridae associated with acute gastroenteritis in humans. Journal of Virology 72:8408–8412
     [Google Scholar]
  54. Yu C. I., Song Y. L. 2000; Outbreaks of Taura syndrome in pacific white shrimp Penaeus vannamei cultured in Taiwan. Fish Pathology 35:21–24
     [Google Scholar]
  55. Zuker M., Mathews D. H., Turner D. H. 1999; Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In RNA Biochemistry and Biotechnology pp 11–43 Edited by Barciszewski J., Clark B. F. C. Dordrecht: Kluwer;
     [Google Scholar]
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Shrimp Taura syndrome virus: genomic characterization and similarity with members of the genus Cricket paralysis-like viruses
J. Gen. Virol. 83, 915 (2002); https://doi.org/10.1099/0022-1317-83-4-915
/content/journal/jgv/10.1099/0022-1317-83-4-915
/content/journal/jgv/10.1099/0022-1317-83-4-915
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