title: Prediction of the structure of the common perimitochondrial localization signal of nuclear transcripts in yeast.
abstract: 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.
authors: Institute of Genetics and Biotechnology, University of Warsaw, Warszawa, Poland.
authors: Radoslaw K
authors: RK
authors: Ejsmont
authors: Pawel
authors: P
authors: Golik
authors: Piotr P
authors: PP
authors: Stepien
mesh_terms: D020413:3' Untranslated Regions; D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics*; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D030561:Databases, Nucleic Acid; D016681:Genome, Fungal; D008928:Mitochondria / Q000502:physiology*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D012331:RNA, Fungal / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D015398:Signal Transduction; D014158:Transcription, Genetic
chemical_list: D020413:3' Untranslated Regions; D004271:DNA, Fungal; D004272:DNA, Mitochondrial; D012331:RNA, Fungal; D029701:Saccharomyces cerevisiae Proteins