Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts

RNA

Volumn 10, Issue 5, 2004, Pages 779-786

  Hatakeyama, Yoshinori ^a,b   Shibuya, Norihiro ^a   Nishiyama, Takashi ^a   Nakashima, Nobuhiko ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b Rational Evol Des Adv Biomolec   (Japan)

Author keywords

Computational search; Dicistroviridae; IRES; Scan For Matches

Indexed keywords

COMPLEMENTARY DNA; RNA; TRANSFER RNA;

ACUTE BEE PARALYSIS VIRUS; ARTICLE; COMPUTER PROGRAM; DICISTROVIRIDAE; EUKARYOTE; GENETIC TRANSCRIPTION; GENOME; INTERNAL RIBOSOME ENTRY SITE; NONHUMAN; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA TRANSLATION; RNA VIRUS; TAURA SYNDROME VIRUS; VIRUS;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; RIBOSOMES; RNA; RNA VIRUSES; SEQUENCE ANALYSIS, RNA;

ACUTE BEE PARALYSIS VIRUS; APOIDEA; DICISTROVIRIDAE; EUKARYOTA; RNA VIRUSES; TAURA SYNDROME VIRUS; TOBACCO STREAK VIRUS;

EID: 1942437439     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5208104     Document Type: Article

References (30)

1. Bakonyi, T., Grabensteiner, E., Kolodziejek, J., Rusvai, M., Topolska, G., Ritter, W., and Nowotny, N. 2002. Phylogenetic analysis of acute bee paralysis virus strains. Appl. Environ. Microbiol. 68: 6446-6450.
2. Bonnal, S., Boutonnet, C., Prado-Lourenco, L., and Vagner, S. 2003. IRESdb: The internal ribosome entry site database. Nucleic Acids Res. 31: 427-428.
3. Domier, L.L., McCoppin, N.K., and D'Arcy, C.J. 2000. Sequence requirements for translation initiation of Rhopalosiphum padi virus ORF 2. Virology 268: 264-271.
4. Drabkin, H.J., Estrella, M., and RajBhandary, U.L. 1998. Initiator-elongator discrimination in vertebrate tRNAs for protein synthesis. Mol. Cell. Biol. 18: 1459-1466.
5. Dsouza, M., Larsen, N., and Overbeek, R. 1997. Searching for patterns in genomic data. Trends Genet. 13: 497-498.
6. Gerlitz, G., Jagus, R., and Elroy-Stein, O. 2002. Phosphorylation of initiation factor-2α is required for activation of internal translation initiation during cell differentiation. Eur. J. Biochem. 269: 2810-2819.
7. Govan, V.A., Leat, N., Allsopp, M., and Davison, S. 2000. Analysis of the complete genome sequence of acute bee paralysis virus shows that it belongs to the novel group of insect-infecting RNA viruses. Virology 277: 457-463.
8. Grillo, G., Licciulli, F., Liuni, S., Sbisa, E., and Pesole, G. 2003. Pat-Search: A program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res. 31: 3608-3612.
9. Hellen, C.U.T. and Sarnow, P. 2001. Internal ribosome entry sites in eukaryotic mRNA molecules. Genes & Dev. 15: 1593-1612.
10. Jan, E. and Sarnow, P. 2002. Factorless ribosome assembly on the internal ribosome entry site of Cricket paralysis virus. J. Mol. Biol. 324: 889-902.
11. Jan, E., Kinzy T.G., and Sarnow, P. 2003. Divergent tRNA-like element supports initiation, elongation, and termination of protein biosynthesis. Proc. Natl. Acad. Sci. 100: 15410-15415.
12. Jang, S.K., Krausslich, H.G., Nicklin, M.J.H., Duke, G.M., Palmenberg, A.C., and 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.
13. Kanamori, Y. and Nakashima, N. 2001. A tertiary structure model of the internal ribosome entry site (IRES) for methionine-independent initiation of translation. RNA 7: 266-274.
14. Kozak, M. 1999. Initiation of translation in prokaryotes and eukaryotes. Gene 234: 187-208.
15. Mari, J., Poulos, B.T., Lightner, D.V., and Bonami, J-R. 2002. Shrimp Taura syndrome virus: Genomic characterization and similarity with members of the genus Cricket paralysis-like viruses. J. Gen. Virol. 83: 915-926.
16. Masoumi, A., Hanzlik, T.N., and Christian, P.D. 2003. Functionality of the 5′- and intergenic IRES elements of cricket paralysis virus in a range of insect cell lines, and its relationship with viral activities. Virus Res. 94: 113-120.
17. Mayo, M.A. 2002. A summary of taxonomic changes recently approved by ICTV. Arch Virol. 147: 1655-1656.
18. McCarthy, J.E.G. 2000. Translation initiation: Insect virus RNAs rewrite the rule book. Curr. Biol. 10: R715-R717.
19. Nishiyama, T., Yamamoto, H., Shibuya, N., Hatakeyama, Y., Hachimori, A., Uchiumi, T., and Nakashima, N. 2003. Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes. Nucleic Acids Res. 31: 2434-2442.
20. Pe'ery, T. and Mathews, M.B. 2000. Viral translational strategies and host defense mechanisms. In Translational control of gene expression (eds. N. Sonenberg et al.), pp. 371-424. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
21. Pelletier, J. and Sonenberg, N. 1988. Internal initiation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature 334: 320-325.
22. Pesole, G., Liuni, S., and D'Souza, M. 2000. PatSearch: A pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance. Bioinformatics 16: 439-450.
23. Pestova, T.V. and Hellen, C.U.T. 2003. Translation elongation after assembly of ribosomes on the Cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA. Genes & Dev. 17: 181-186.
24. Sasaki, J. and 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. J. Virol. 73: 1219-1226.
25. -. 2000. Methionine-independent initiation of translation in the capsid protein of an insect RNA virus. Proc. Natl Acad. Sci. 97: 1512-1515.
26. Shibuya, N., Nishiyama, T., Kanamori, Y., Saito, H., and Nakashima, N. 2003. Conditional rather than absolute requirements of the capsid coding sequence for initiation of methionine-independent translation in Plautia stali intestine virus. J. Virol. 77: 12002-12010.
27. Thompson, S.R., Gulyas, K.D., and Sarnow P. 2001. Internal initiation in Saccharomyces cerevisiae mediated by an initiator tRNA/eIF2-independent internal ribosome entry site element. Proc. Natl. Acad. Sci. 98: 12972-12977.
28. Vagner, S., Galy, B., and Pyronnet, S. 2001. Irresistible IRES, attracting the translation machinery to internal ribosome entry sites. EMBO Rep. 2: 893-898.
29. Wilson, J.E., Pestova, T.V., Hellen, C.U.T., and Sarnow, P. 2000a. Initiation of protein synthesis from the A site of the ribosome. Cell 102: 511-520.
30. Wilson, J.E., Powell, M.J., Hoover, S.E., and Sarnow, P. 2000b. Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol. Cell. Biol. 20: 4990-4999.