The untranslated regions of mRNA molecules are involved in several posttranscriptional regulatory pathways. The 5’UTR is the sequence between the 5’ terminal cap structure and the initiation codon for protein synthesis. The 5’ end (the leader) can accurately regulate the amount of protein synthesised from a specific mRNA. In a fraction of mRNAs, upstream open reading frames (uORFs) are present. A general method for detecting uORFs with a regulatory role is of great importance. The ribosome can recognise the AUG of a uORF as an initiation codon, translate the downstream sequence into protein and terminate before the main ORF is translated.
Although the complete genome of the yeast Saccharomyces cerevisiae has been sequenced, the number of mRNAs containing uORFs is not known. It is predicted that in S.cerevisiae 200 genes (3 %) have uORFs. The facts that mRNA start sites are not known, and that some genes have more than one promoter, constitute major problems in the
identification of real uORFs. In this study, a collection of 18 genes with known uORFs was examined. It has been observed that some genes have a very long leader (CLN3 – 864nt), while some are extremely short (DCD1 – 33nt). Also, a longer UTR doesn’t necessarily correlate to a longer uORF or higher uORF frequency (CLN3 – UTR 864nt, one uORF – 4 codons long). A comparative analysis has been done for the yeast Saccharomyces cerevisiae and six related species (S. paradoxus, S. mikatae, S. bayanus, S. castellii, S. kluyveri, S. kudriavzevii). We aligned sequences (1000 nt upstream of the initiation codon) using a pairwise sequence alignment method, and then labelled all identified uORFs. It has been observed that uORFs in some genes, where a functional role for the uORFs had been established by experiment, show a striking conservation. Upstream ORFs from other genes, where no indication of such regulation was available, displayed a lower degree of conservation. |