IRES-dependent translated genes in fungi: computational prediction, phylogenetic conservation and functional association

Background The initiation of translation via cellular internal ribosome entry sites plays an important role in the stress response and certain physiological conditions in which canonical cap-dependent translation initiation is compromised. Currently, only a limited number of these regulatory elements have been experimentally identified. Notably, cellular internal ribosome entry sites lack conservation of both the primary sequence and mRNA secondary structure, rendering their identification difficult. Despite their biological importance, the currently available computational strategies to predict them have had limited success. We developed a bioinformatic method based on a support vector machine for the prediction of internal ribosome entry sites in fungi using the 5’-UTR sequences of 20 non-redundant fungal organisms. Additionally, we performed a comparative analysis and characterization of the functional relationships among the gene products predicted to be translated by this cap-independent mechanism.