mRNA translation and turnover: a cellular perspective on their relationship

The rate at which a protein is synthesized is influenced by the stability of its mRNA and the efficiency of translation. mRNA degradation is associated with translation, but the link between these processes is unclear. In this article, Alistair Brown discusses this relationship in the light of a model of translation that involves three distinct cellular phases: a primary phase in which the translation of an mRNA molecule starts before its export from the nucleus is complete, a secondary phase that begins when nuclear export is complete and that may involve circular polyribosomal complexes, and a terminal phase involving residual translation once mRNA degradation is initiated.     

Analysis and prediction of translation rate based on sequence and functional features of the mRNA

Protein concentrations depend not only on the mRNA level, but also on the translation rate and the degradation rate. Prediction of mRNA's translation rate would provide valuable information for in-depth understanding of the translation mechanism and dynamic proteome. In this study, we developed a new computational model to predict the translation rate, featured by (1) integrating various sequence-derived and functional features, (2) applying the maximum relevance & minimum redundancy method and incremental feature selection to select features to optimize the prediction model, and (3) being able to predict the translation rate of RNA into high or low translation rate category. The prediction accuracies under rich and starvation condition were 68.8% and 70.0%, respectively, evaluated by jackknife cross-validation. It was found that the following features were correlated with translation rate: codon usage frequency, some gene ontology enrichment scores, number of RNA binding proteins known to bind its mRNA product, coding sequence length, protein abundance and 5'UTR free energy. These findings might provide useful information for understanding the mechanisms of translation and dynamic proteome. Our translation rate prediction model might become a high throughput tool for annotating the translation rate of mRNAs in large-scale.