1887

Abstract

picorna-like virus (EoPV) is a newly described insect virus that is classified as a putative member of the genus . The virus possesses a large, positive-sense RNA genome encoding a single polyprotein that shares physicochemical properties with those of members of the family . The 5′ untranslated region (5′ UTR) plays an important role in picornavirus translation initiation, as it contains an internal ribosome entry site (IRES) that mediates cap-independent translation. To investigate translation in EoPV, an extensive range of mutations were engineered within the 5′ UTR and the effects of these changes were examined and by using a bicistronic construct. Results showed that deletions within the first 63 nt had little impact on IRES activity, whilst core IRES function was contained within stem–loops C and D, as their removal abrogated IRES activity significantly. In contrast to these findings, removal of stem–loop G containing two cryptic AUGs caused a remarkable increase in IRES activity, which was further investigated by site-directed mutagenesis at these two positions. It was also confirmed that initiation of protein synthesis occurs at AUG6 (position 391–394) and not at the AUG immediately downstream of the polypyrimidine tract. Mutation of the polypyrimidine tract (CCTTTC) had a slight effect on EoPV IRES activity. Furthermore, mutations of the RAAA motif led to a decrease in IRES activity of approximately 40 % , but these results were not supported by experiments. In conclusion, this study reveals that the EoPV IRES element is unique, although it has features in common with the type II IRESs.

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2006-12-01
2024-03-29
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References

  1. Agol V. I. 1991; The 5′-untranslated region of picornaviral genomes. Adv Virus Res 40:103–180
    [Google Scholar]
  2. Belsham G. J. 1992; Dual initiation sites of protein synthesis on foot-and-mouth disease virus RNA are selected following internal entry and scanning of ribosomes in vivo . EMBO J 11:1105–1110
    [Google Scholar]
  3. Belsham G. J., Brangwyn J. K. 1990; A region of the 5′ noncoding region of foot-and-mouth disease virus RNA directs efficient internal initiation of protein synthesis within cells: involvement with the role of L protease in translational control. J Virol 64:5389–5395
    [Google Scholar]
  4. Belsham G. J., Jackson R. J. 2000; Translation initiation on picornavirus RNA. In Translational Control of Gene Expression pp  869–900 Edited by Sonenberg N., Hershey J. W. B., Mathews M. B. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  5. Belsham G. J., Sonenberg N. 2000; Picornavirus RNA translation: roles for cellular proteins. Trends Microbiol 8:330–335 [CrossRef]
    [Google Scholar]
  6. Brown E. A., Day S. P., Jansen R. W., Lemon S. M. 1991; The 5′ nontranslated region of hepatitis A virus RNA: secondary structure and elements required for translation in vitro. J Virol 65:5828–5838
    [Google Scholar]
  7. Brown E. A., Zajac A. J., Lemon S. M. 1994; In vitro characterization of an internal ribosomal entry site (IRES) present within the 5′ nontranslated region of hepatitis A virus RNA: comparison with the IRES of encephalomyocarditis virus. J Virol 68:1066–1074
    [Google Scholar]
  8. Carter M. S., Sarnow P. 2000; Distinct mRNAs that encode La autoantigen are differentially expressed and contain internal ribosome entry sites. J Biol Chem 275:28301–28307
    [Google Scholar]
  9. Chard L. S., Bordeleau M.-E., Pelletier J., Tanaka J., Belsham G. J. 2006a; Hepatitis C virus-related internal ribosome entry sites are found in multiple genera of the family Picornaviridae . J Gen Virol 87:927–936 [CrossRef]
    [Google Scholar]
  10. Chard L. S., Kaku Y., Jones B., Nayak A., Belsham G. J. 2006b; Functional analyses of RNA structures shared between the internal ribosome entry sites of hepatitis C virus and the picornavirus porcine teschovirus 1 Talfan. J Virol 80:1271–1279 [CrossRef]
    [Google Scholar]
  11. Christian P., Carstens E., Domier L., Johnson K., Nakashima N., Scotti P., van der Wilk F. 2002; Infectious flacherie-like viruses. ICTV Virus Taxonomy 2002 www.ictvdb.iacr.ac.uk/Ictv/index.htm
    [Google Scholar]
  12. De Rijk P., Wuyts J., De Wachter R. 2003; RnaViz 2: an improved representation of RNA secondary structure. Bioinformatics 19:299–300 [CrossRef]
    [Google Scholar]
  13. Dever T. E. 2002; Gene-specific regulation by general translation factors. Cell 108:545–556 [CrossRef]
    [Google Scholar]
  14. Duke G. M., Hoffman M. A., Palmenberg A. C. 1992; Sequence and structural elements that contribute to efficient encephalomyocarditis virus RNA translation. J Virol 66:1602–1609
    [Google Scholar]
  15. Fletcher S. P., Jackson R. J. 2002; Pestivirus internal ribosome entry site (IRES) structure and function: elements in the 5′ untranslated region important for IRES function. J Virol 76:5024–5033 [CrossRef]
    [Google Scholar]
  16. Fujiyuki T., Takeuchi H., Ono M., Ohka S., Sasaki T., Nomoto A., Kubo T. 2004; Novel insect picorna-like virus identified in the brains of aggressive worker honeybees. J Virol 78:1093–1100 [CrossRef]
    [Google Scholar]
  17. 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. J Gen Virol 80:1541–1549
    [Google Scholar]
  18. Glass M. J., Jia X.-Y., Summers D. F. 1993; Identification of the hepatitis A virus internal ribosome entry site: in vivo and in vitro analysis of bicistronic RNAs containing the HAV 5′ noncoding region. Virology 193:842–852 [CrossRef]
    [Google Scholar]
  19. Haller A. A., Nguyen J. H. C., Semler B. L. 1993; Minimum internal ribosome entry site required for poliovirus infectivity. J Virol 67:7461–7471
    [Google Scholar]
  20. Hashimoto Y., Watanabe A., Kawase S. 1984; In vitro translation of infectious flacherie virus RNA in a wheat germ and a rabbit reticulocyte system. Biochim Biophys Acta 781:76–80 [CrossRef]
    [Google Scholar]
  21. Hershey J. W. B., Merrick W. C. 2000; Pathway and mechanism of initiation of protein synthesis. In Translational Control of Gene Expression pp  33–88 Edited by Sonenberg N., Hershey J. W. B., Mathews M. B. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  22. Hinton T. M., Li F., Crabb B. S. 2000; Internal ribosomal entry site-mediated translation initiation in equine rhinitis A virus: similarities to and differences from that of foot-and-mouth disease virus. J Virol 74:11708–11716 [CrossRef]
    [Google Scholar]
  23. Hoffman M. A., Palmenberg A. C. 1995; Mutational analysis of the J-K stem-loop region of the encephalomyocarditis virus IRES. J Virol 69:4399–4406
    [Google Scholar]
  24. Hunt S. L., Jackson R. J. 1999; Polypyrimidine-tract binding protein (PTB) is necessary, but not sufficient, for efficient internal initiation of translation of human rhinovirus-2 RNA. RNA 5:344–359 [CrossRef]
    [Google Scholar]
  25. 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. Arch Virol 143:127–143 [CrossRef]
    [Google Scholar]
  26. Jackson R. J., Kaminski A. 1995; Internal initiation of translation in eukaryotes: the picornavirus paradigm and beyond. RNA 1:985–1000
    [Google Scholar]
  27. Jackson R. J., Hunt S. L., Gibbs C. L., Kaminski A. 1994; Internal initiation of translation of picornavirus RNAs. Mol Biol Rep 19:147–159 [CrossRef]
    [Google Scholar]
  28. Jang S. K., Wimmer E. 1990; Cap-independent translation of encephalomyocarditis virus RNA: structural elements of the internal ribosomal entry site and involvement of a cellular 57-kD RNA-binding protein. Genes Dev 4:1560–1572 [CrossRef]
    [Google Scholar]
  29. Jang S. K., Kräusslich H.-G., Nicklin M. J. H., Duke G. M., Palmenberg A. C., Wimmer E. 1988; A segment of the 5′ nontranslated region of encephalomyocarditis virus RNA directs internal entry of ribosomes during in vitro translation. J Virol 62:2636–2643
    [Google Scholar]
  30. Jang S. K., Davies M. V., Kaufman R. J., Wimmer E. 1989; Initiation of protein synthesis by internal entry of ribosomes into the 5′ nontranslated region of encephalomyocarditis virus RNA in vivo. J Virol 63:1651–1660
    [Google Scholar]
  31. Jang S. K., Pestova T. V., Hellen C. U. T., Witherell G. W., Wimmer E. 1990; Cap-independent translation of picornavirus RNAs: structure and function of the internal ribosomal entry site. Enzyme 44:292–309
    [Google Scholar]
  32. Kaku Y., Chard L. S., Inoue T., Belsham G. J. 2002; Unique characteristics of a picornavirus internal ribosome entry site from the porcine teschovirus-1 Talfan. J Virol 76:11721–11728 [CrossRef]
    [Google Scholar]
  33. Kaminski A., Belsham G. J., Jackson R. J. 1994; Translation of encephalomyocarditis virus RNA: parameters influencing the selection of the internal initiation site. EMBO J 13:1673–1681
    [Google Scholar]
  34. Kühn R., Luz N., Beck E. 1990; Functional analysis of the internal translation initiation site of foot-and-mouth disease virus. J Virol 64:4625–4631
    [Google Scholar]
  35. Lanzi G., de Miranda J. R., Boniotti M. B., Cameron C. E., Lavazza A., Capucci L., Camazine S. M., Rossi C. 2006; Molecular and biological characterization of deformed wing virus of honeybees ( Apis mellifera L.). J Virol 80:4998–5009 [CrossRef]
    [Google Scholar]
  36. López de Quinto S., Martínez-Salas E. 1997; Conserved structural motifs located in distal loops of aphthovirus internal ribosome entry site domain 3 are required for internal initiation of translation. J Virol 71:4171–4175
    [Google Scholar]
  37. Mathews D. H., Sabina J., Zuker M., Turner D. H. 1999; Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288:911–940 [CrossRef]
    [Google Scholar]
  38. Meerovitch K., Sonenberg N. 1993; Internal initiation of picornavirus RNA translation. Semin Virol 4:217–227 [CrossRef]
    [Google Scholar]
  39. Meerovitch K., Nicholson R., Sonenberg N. 1991; In vitro mutational analysis of cis -acting RNA translational elements within the poliovirus type 2 5′ untranslated region. J Virol 65:5895–5901
    [Google Scholar]
  40. Nicholson R., Pelletier J., Le S.-Y., Sonenberg N. 1991; Structural and functional analysis of the ribosome landing pad of poliovirus type 2: in vivo translation studies. J Virol 65:5886–5894
    [Google Scholar]
  41. Nicklin M. J. H., Kräusslich H. G., Toyoda H., Dunn J. J., Wimmer E. 1987; Poliovirus polypeptide precursors: expression in vitro and processing by exogenous 3C and 2A proteinases. Proc Natl Acad Sci U S A 84:4002–4006 [CrossRef]
    [Google Scholar]
  42. Niklasson B., Kinnunen L., Hörnfeldt B., Hörling J., Benemar C., Hedlund K. O., Matskova L., Hyypiä T., Winberg G. 1999; A new picornavirus isolated from bank voles ( Clethrionomys glareolus ). Virology 255:86–93 [CrossRef]
    [Google Scholar]
  43. Ongus J. R., Peters D., Bonmatin J.-M., Bengsch E., Vlak J. M., van Oers M. M. 2004; Complete sequence of a picorna-like virus of the genus Iflavirus replicating in the mite Varroa destructor . J Gen Virol 85:3747–3755 [CrossRef]
    [Google Scholar]
  44. Palmenberg A. C., Sgro J.-Y. 1997; Topological organization of picornaviral genomes: statistical prediction of RNA structural signals. Semin Virol 8:231–241 [CrossRef]
    [Google Scholar]
  45. Pelletier J., Sonenberg N. 1988; Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature 334:320–325 [CrossRef]
    [Google Scholar]
  46. Percy N., Belsham G. J., Brangwyn J. K., Sullivan M., Stone D. M., Almond J. W. 1992; Intracellular modifications induced by poliovirus reduce the requirement for structural motifs in the 5′ noncoding region of the genome involved in internal initiation of protein synthesis. J Virol 66:1695–1701
    [Google Scholar]
  47. Pestova T. V., Hellen C. U. T., Wimmer E. 1991; Translation of poliovirus RNA: role of an essential cis -acting oligopyrimidine element within the 5′ nontranslated region and involvement of a cellular 57-kilodalton protein. J Virol 65:6194–6204
    [Google Scholar]
  48. Pestova T. V., Shatsky I. N., Fletcher S. P., Jackson R. J., Hellen C. U. T. 1998; A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initation of hepatitis C and classical swine fever virus RNAs. Genes Dev 12:67–83 [CrossRef]
    [Google Scholar]
  49. Pilipenko E. V., Blinov V. M., Chernov B. K., Dmitrieva T. M., Agol V. I. 1989; Conservation of the secondary structure elements of the 5′-untranslated region of cardio- and aphthovirus RNAs. Nucleic Acids Res 17:5701–5711 [CrossRef]
    [Google Scholar]
  50. Pilipenko E. V., Gmyl A. P., Maslova S. V., Svitkin Y. V., Sinyakov A. N., Agol V. I. 1992; Prokaryotic-like cis elements in the cap-independent internal initiation of translation on picornavirus RNA. Cell 68:119–131 [CrossRef]
    [Google Scholar]
  51. Pisarev A. V., Chard L. S., Kaku Y., Johns H. L., Shatsky I. N., Belsham G. J. 2004; Functional and structural similarities between the internal ribosome entry sites of hepatitis C virus and porcine teschovirus, a picornavirus. J Virol 78:4487–4497 [CrossRef]
    [Google Scholar]
  52. Sarnow P. 2003; Viral internal ribosome entry site elements: novel ribosome-RNA complexes and roles in viral pathogenesis. J Virol 77:2801–2806 [CrossRef]
    [Google Scholar]
  53. Stanway G., Joki-Korpela P., Hyypiä T. 2000; Human parechoviruses – biology and clinical significance. Rev Med Virol 10:57–69 [CrossRef]
    [Google Scholar]
  54. Stewart S. R., Semler B. L. 1997; RNA determinants of picornavirus cap-independent translation initiation. Semin Virol 8:242–255 [CrossRef]
    [Google Scholar]
  55. Todd S., Towner J. S., Semler B. L. 1997; Translation and replication properties of the human rhinovirus genome in vivo and in vitro . Virology 229:90–97 [CrossRef]
    [Google Scholar]
  56. van Poelwijk F., Broer R., Belsham G. J., Oudshoorn P., Vlak J. M., Goldbach R. W. 1995; A hybrid baculovirus-bacteriophage T7 transient expression system. Biotechnology 13:261–264 [CrossRef]
    [Google Scholar]
  57. Wang X., Zhang J., Lu J., Yi F., Liu C., Hu Y. 2004; Sequence analysis and genomic organization of a new insect picorna-like virus, Ectropis obliqua picorna-like virus, isolated from Ectropis obliqua . J Gen Virol 85:1145–1151 [CrossRef]
    [Google Scholar]
  58. Witherell G. W., Schultz-Witherell C. S., Wimmer E. 1995; cis -Acting elements of the encephalomyocarditis virus internal ribosomal entry site. Virology 214:660–663 [CrossRef]
    [Google Scholar]
  59. Wu C.-Y., Lo C.-F., Huang C.-J., Yu H.-T., Wang C.-H. 2002; The complete genome sequence of Perina nuda picorna-like virus, an insect-infecting RNA virus with a genome organization similar to that of the mammalian picornaviruses. Virology 294:312–323 [CrossRef]
    [Google Scholar]
  60. 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 Barciszwski J., Clark B. F. C. Dordrecht: Kluwer Academic Publishers;
    [Google Scholar]
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