Polycistronic mRNAs transcribed from operons are resolved into translatable monocistrons by the trans-splicing of a separately transcribed spliced leader (SL) RNA. The SL then forms the 5’ ends of resulting monocistrons. The SL is also trans-spliced to non-operon mRNAs where its function has long remained mysterious. The phylogenetic distribution of trans-splcing is disparate and it is found in O. dioica.
A switch in the use of trans-splicing at the maternal to zygotic transition
We used a modifed cap analysis of gene expression (CAGE) in order to map and explore trans-splicing in O. dioica. We discovered a remarkable shift in the use of trans-splicing at the maternal to zygotic transition: the majority of maternal mRNAs are trans-spliced whereas the majority of mRNAs produced after the activation of the zygotic genome are not. Furthermore, we found a similar maternal enrichment in two other metazoan species suggesting that this feature drives the evolution, or retention, of trans-splicing in animal genomes.
Nutrient-dependent translational control via the SL
Our analysis also showed that the majority of ribosomal protein mRNAs are trans-spliced in O. dioica. These mRNAs in other species contain a highly conserved 5’ Terminal OligoPyrimidine (TOP) motif, which is essential to their translational suppression via the central regulator of growth, mTOR (mechanistic Target Of Rapamycin), when growth conditions are unfavorable. This leads to the suppression of the costly process of protein synthesis. Since these TOP mRNAs are trans-spliced in O. dioica and the SL constitutes their 5’ ends we hypothesized that the 5’ end of the SL replaces the function of the TOP motif and permits the nutrient-dependent translational control of maternal mRNA, via mTOR. This may be the molecular mechanism for adjusting egg numbers according to nutrient levels. Furthermore, trans-splicing translational control motifs, rather than encoding them at individual loci, allows for the spatial and developmental regulation of mTOR targets: trans-splice sites can be excluded by the use of alternative promoters. The generation or loss of new targets for nutrient-dependent translational control would require only the gain or loss of a trans-splice site within a gene. This may allow high plasticity in the evolution of a nutrient-dependent translational response.
We are testing the use of nutrient-dependent translational control via the spliced leader using a combination of molecular methods, including ribosome profiling.
G.B. Danks, M. Raasholm, C. Campsteijn, A.M. Long, J.R. Manak, B. Lenhard, and E.M. Thompson. Trans-splicing and operons in metazoans: Translational control in maternally regulated development and recovery from growth arrest. Molecular Biology and Evolution, 32(3), 2015.