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

被引:40
作者
Hatakeyama, Y [1 ]
Shibuya, N [1 ]
Nishiyama, T [1 ]
Nakashima, N [1 ]
机构
[1] Natl Inst Agrobiol Sci, Tsukuba, Ibaraki 3058634, Japan
关键词
IRES; dicistroviridae; computational search; scan for matches;
D O I
10.1261/rna.5208104
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The intergenic region (IGR) located upstream of the capsid protein gene in dicistroviruses contains an internal ribosome entry site (IRES). Translation initiation mediated by the IRES does not require initiator methionine tRNA. Comparison of the IGRs among dicistroviruses suggested that Taura syndrome virus (TSV) and acute bee paralysis virus have an extra side stem loop in the predicted IRES. We examined whether the side stem is responsible for translation activity mediated by the IGR using constructs with compensatory mutations. In vitro translation analysis showed that TSV has an IGR-IRES that is structurally distinct from those previously described. Because IGR-IRES elements determine the translation initiation site by virtue of their own tertiary structure formation, the discovery of this initiation mechanism suggests the possibility that eukaryotic mRNAs might have more extensive coding regions than previously predicted. To test this hypothesis, we searched full-length cDNA databases and whole genome sequences of eukaryotes using the pattern matching program, Scan For Matches, with parameters that can extract sequences containing secondary structure elements resembling those of IGR-IRES. Our search yielded several sequences, but their predicted secondary structures were suggested to be unstable in comparison to those of dicistroviruses. These results suggest that RNAs structurally similar to dicistroviruses are not common. If some eukaryotic mRNAs are translated independently of an initiator methionine tRNA, their structures are likely to be significantly distinct from those of dicistroviruses.
引用
收藏
页码:779 / 786
页数:8
相关论文
共 30 条
[1]   Phylogenetic analysis of acute bee paralysis virus strains [J].
Bakonyi, T ;
Grabensteiner, E ;
Kolodziejek, J ;
Rusvai, M ;
Topolska, G ;
Ritter, W ;
Nowotny, N .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2002, 68 (12) :6446-6450
[2]   IRESdb:: the internal ribosome entry site database [J].
Bonnal, S ;
Boutonnet, C ;
Prado-Lourenço, L ;
Vagner, S .
NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :427-428
[3]   Sequence requirements for translation initiation of Rhopalosiphum padi virus ORF2 [J].
Domier, LL ;
McCoppin, NK ;
D'Arcy, CJ .
VIROLOGY, 2000, 268 (02) :264-271
[4]   Initiator-elongator discrimination in vertebrate tRNAs for protein synthesis [J].
Drabkin, HJ ;
Estrella, M ;
Rajbhandary, UL .
MOLECULAR AND CELLULAR BIOLOGY, 1998, 18 (03) :1459-1466
[5]   Searching for patterns in genomic data [J].
Dsouza, M ;
Larsen, N ;
Overbeek, R .
TRENDS IN GENETICS, 1997, 13 (12) :497-498
[6]   Phosphorylation of initiation factor-2α is required for activation of internal translation initiation during cell differentiation [J].
Gerlitz, G ;
Jagus, R ;
Elroy-Stein, O .
EUROPEAN JOURNAL OF BIOCHEMISTRY, 2002, 269 (11) :2810-2819
[7]   Analysis of the complete genome sequence of acute bee paralysis virus shows that it belongs to the novel group of insect-infecting RNA viruses [J].
Govan, VA ;
Leat, N ;
Allsopp, M ;
Davison, S .
VIROLOGY, 2000, 277 (02) :457-463
[8]   PatSearch:: a program for the detection of patterns and structural motifs in nucleotide sequences [J].
Grillo, G ;
Licciulli, F ;
Liuni, S ;
Sbisà, E ;
Pesole, G .
NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3608-3612
[9]   Internal ribosome entry sites in eukaryotic mRNA molecules [J].
Hellen, CUT ;
Sarnow, P .
GENES & DEVELOPMENT, 2001, 15 (13) :1593-1612
[10]   Divergent tRNA-like element supports initiation, elongation, and termination of protein biosynthesis [J].
Jan, E ;
Kinzy, TG ;
Sarnow, P .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (26) :15410-15415