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

Abstract

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.

Results: Using our method, we predicted 6,532 internal ribosome entry sites in 20 non-redundant fungal organisms. Some orthologous groups were enriched with our positive predictions. This is the case of the HSP70 chaperone family, which remarkably has two verified internal ribosome entry sites, one in humans and the other in flies. A second example is the orthologous group of the eIF4G repression protein Sbp1p, which has two homologous genes known to be translated by this cap-independent mechanism, one in mice and the other in yeast. These examples emphasize the wide conservation of these regulatory elements as a result of selective pressure. In addition, we performed a protein-protein interaction network characterization of the gene products of our positive predictions using Saccharomyces cerevisiae as a model, which revealed a highly connected and modular topology, suggesting a functional association. A remarkable example of this functional association is our prediction of internal ribosome entry sites elements in three components of the RNA polymerase II mediator complex.

Conclusions: We developed a method for the prediction of cellular internal ribosome entry sites that may guide experimental and bioinformatic analyses to increase our understanding of protein translation regulation. Our analysis suggests that fungi show evolutionary conservation and functional association of proteins translated by this cap-independent mechanism.

Fig. 1

Predictions of enriched orthologous groups. Some of the most relevant groups are labeled. The statistical significance of the enriched orthologous groups is highlighted. The number of predictions within each group is proportional to the size of the points

Fig. 2

GO-term enrichment analysis for the top IRES predictions. The GO-term enrichment analysis was performed using the GOstats package for R. Fold enrichment values are represented as the minus base 10 log of their corresponding p-values

Fig. 3

Network clustering of the proteins translated by the set of top IRES predictions in S. cerevisiae. Each group is represented by a different color (a) GO-term enrichment analysis. The p-values of the GO-term enrichments are represented in logarithmic terms. b PPI network. The size of each vertex is proportional to its connectivity degree value. c Number of proteins in each module. d Node connectivity distribution by module

Fig. 4

PPI network density of the predicted proteins compared with simulated random networks. The full network and the modules are more cohesive than random networks