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2007 | 54 | 1 | 55-61
Article title

Prediction of the structure of the common perimitochondrial localization signal of nuclear transcripts in yeast

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Many nuclear genes encoding mitochondrial proteins require specific localization of their mRNAs to the vicinity of mitochondria for proper expression. Studies in Saccharomyces cerevisiae have shown that the cis-acting signal responsible for subcellular localization of mRNAs is localized in the 3' UTR of the transcript. In this paper we present an in silico approach for prediction of a common perimitochondrial localization signal of nuclear transcripts encoding mitochondrial proteins. We computed a consensus structure for this signal by comparison of 3' UTR models for about 3000 yeast transcripts with known localization. Our studies show a short stem-loop structure which appears in most mRNAs localized to the vicinity of mitochondria. The degree of similarity of a given 3' UTR to our consensus structure strongly correlates with experimentally determined perimitochondrial localization of the mRNA, therefore we believe that the structure we predicted acts as a subcellular localization signal. Since our algorithm operates on structures, it seems to be more reliable than sequence-based algorithms. The good predictive value of our model is supported by statistical analysis.
Physical description
  • Institute of Genetics and Biotechnology, University of Warsaw, Warszawa, Poland
  • Institute of Genetics and Biotechnology, University of Warsaw, Warszawa, Poland
  • Institute of Genetics and Biotechnology, University of Warsaw, Warszawa, Poland
  • Caballero JJ, Giron MD, Vargas AM, Sevillano N, Suarez MD, Salto R (2004) AU-rich elements in the mRNA 3'-untranslated region of the rat receptor for advanced glycation end products and their relevance to mRNA stability. Biochem Biophys Res Commun 319: 247-255.
  • Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D (1997) Genetic and physical maps of Saccharomyces cerevisiae. Nature 387: 67-73.
  • Corral-Debrinski M, Blugeon C, Jacq C (2000) In yeast the 3'untranslated region or the presequence of ATM1 is required for the exclusive localization of its mRNA to the vicinity of mitochondria. Mol Cell Biol 20: 7881-7892.
  • Gish W (1996-2003) WU-BLAST http://blastwustledu.
  • Graber JH, Cantor CR, Mohr SC, Smith TF (1999) Genomic detection of new yeast pre-mRNA 3'-end-processing signals. Nucleic Acids Res 27: 888-894.
  • Grafi G, Sela I, Galili G (1993) Translational regulation of human beta interferon mRNA: association of the 3' AU-rich sequence with the poly(A) tail reduces translation efficiency in vitro. Mol Cell Biol 13: 3487-3493.
  • Higgins D, Thompson J, Gibson T, Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
  • Hofacker IL (2003) Vienna RNA secondary structure server Nucleic Acids Res 31: 3429-3431.
  • Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK (2003) Global analysis of protein localization in budding yeast. Nature 425: 686-691.
  • Jacobs Anderson JS, Parker R (2000) Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae. Nucleic Acids Res 28: 1604-1617.
  • Jansen RP (2001) mRNA localization: message on the move. Nat Rev Mol Cell Biol 2: 247-256.
  • Legendre M, Gautheret D (2003) Sequence determinants in human polyadenylation site selection. BMC Genomics 4: 7.
  • Marc P, Margeot A, Devaux F, Blugeon C, Corral-Debrinski M, Jacq C (2002) Genome-wide analysis of mRNAs targeted to yeast mitochondria. EMBO Rep 3: 159-164.
  • Margeot A, Blugeon C, Sylvestre J, Vialette S, Jacq C, Corral-Debrinski M (2002) In Saccharomyces cerevisiae ATP2 mRNA sorting to the vicinity of mitochondria is essential for respiratory function. EMBO J 21: 6893-6904.
  • Pesole G, Liuni S, Grillo G, Licciulli F, Mignone F, Gissi C, Saccone C (2002) UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs; Update 2002. Nucleic Acids Res 30: 335-340.
  • Sylvestre J, Margeot A, Jacq C, Dujardin G, Corral-Debrinski M (2003) The role of the 3'untranslated region in mrna sorting to the vicinity of mitochondria is conserved from yeast to human cells. Mol Biol Cell 14: 3848-3856.
  • Yamada M, Hayatsu N, Matsuura A, Ishikawa F (1998) Y'-Help1 a DNA helicase encoded by the yeast subtelomeric Y' element is induced in survivors defective for telomerase. J Biol Chem 273: 33360-33366.
  • Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
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