June 25th
Recent Publications Harnessing the Power of Translatomics.
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers, Bartsch et al. look at translational control in human embryonic stem cells (hESCs), Aksoylu et al. look at the role of translation in neurocutaneous disorder; Tuberous sclerosis complex (TSC). Finally, Bharudin et al. look at the mRNA decapping mechanism involving the of Dcp1-Dcp2 complex in Aspergillus nidulans.
mRNA translational specialization by RBPMS presets the competence for cardiac commitment in hESCs
Science Advances, 2023
Bartsch, D., Kalamkar, K., Ahuja, G., Lackmann, J.W., Hescheler, J., Weber, T., Bazzi, H., Clamer, M., Mendjan, S., Papantonis, A. and Kurian, L.
During embryogenesis, the developmental pathways of organs are believed to be determined by transcriptional and epigenetic mechanisms. However, this study uncovers a novel mechanism involving a specialized mRNA translation circuit controlled by a protein called RBPMS, which pre-establishes the capacity for future cardiac fate in human embryonic stem cells (hESCs) during pluripotency.
This study utilized polysome profiling and translation complex profiling (TCP) to investigate the role of the RNA-binding protein RBPMS in translational control and cellular identity in human embryonic stem cells (hESCs). TCP is a variant of ribosome profiling specifically designed to analyze translation initiation complexes. It involves the isolation and analysis of the fraction containing the 40S ribosomal subunit and the preinitiation complex to gain insights into the composition and abundance of translation initiation factors associated with translationally engaged mRNAs.
The researchers confirmed the recruitment of RBPMS onto ribosomal complexes during pluripotency and demonstrated that loss of RBPMS severely disrupts ribosome recruitment and translation initiation, leading to a significant reduction in global protein synthesis. The analysis of translation initiation complexes revealed the disruption of key components involved in guanosine 5′-triphosphate exchange, EIF3 complex retention, and depletion of EIF5A upon RBPMS loss. These findings highlight the critical role of RBPMS in shaping cellular identity by selectively enhancing the translation of regulatory components and indicate that ribosomes serve as a central hub for cellular decision-making beyond their traditional role in protein synthesis.
Overall, this research highlights the importance of translational specialization in shaping cellular identity during early developmental lineage decisions, suggesting that ribosomes serve as a central hub for cellular decision-making beyond their traditional role as protein synthesis machinery.
Translatome analysis of Tuberous Sclerosis Complex-1 patient-derived neural progenitor cells reveal rapamycin-dependent and independent alterations
Preprint, 2023
Aksoylu, I., Martin, P., Robert, F., Szkop, K., Redmond, N., Chen, S., Beauchamp, R., Nobeli, I., Pelletier, J., Larsson, O. and Ramesh, V.
Tuberous sclerosis complex (TSC) is a hereditary neurocutaneous disorder caused by mutations in the TSC1 or TSC2 genes. Patients with TSC often display neurodevelopmental (ND) symptoms known as TSC-associated neuropsychiatric disorders (TAND), which can include autism spectrum disorder (ASD). The hamartin-tuberin (TSC1-TSC2) protein complex plays a role in deactivating the mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway. This deactivation leads to increased protein synthesis by inhibiting the translational repressor eIF4E-binding proteins (4E-BPs).
The researchers aimed to investigate the effects of TSC1 loss-of-function mutations on mRNA levels and translation in neural progenitor cells (NPCs). They utilized skin fibroblasts from a patient with a specific TSC1 mutation to create isogenic TSC1-null NPCs (−/−) and corrected TSC1-WT NPCs (+/+). To analyze gene expression changes, the researchers performed polysome-profiling.
Loss of TSC1 or TSC2 activates mTORC1 signaling. The mTORC1 pathway is crucial for protein synthesis, and TSC1 loss affects mRNA translation in patient-derived neural progenitor cells (NPCs) and ASD brains. Translational offsetting, an unclear gene expression mode, is also observed. Rapamycin partially reverses TSC1-related gene expression changes but has limited impact on neural activity/synaptic regulation or ASD-related genes. Second-generation mTOR kinase inhibitors inhibit mTORC1 and mTORC2 but with limited efficacy. A third-generation mTORC1-directed inhibitor called RapaLink-1 shows promise in reducing phosphorylation of S6K1 and 4E-BP1 and has antitumor efficacy in glioma models. RMC-6272, a bi-steric mTORC1-selective inhibitor, is more potent than rapamycin, reverses translational changes unaffected by rapamycin, and improves neurodevelopmental phenotypes in TSC1-null NPCs. Dysregulated mTORC1 signaling is observed in other ASD and neuropsychiatric disorders, suggesting a role for cap-dependent translation downstream of mTORC1 in these conditions.
These findings provide insights into the molecular mechanisms underlying TSC1-associated neurodevelopmental disorders and will contribute to understanding the pathophysiology and potentially lead to new therapeutic strategies.
Disruption of Dcp1 leads to a Dcp2‐dependent aberrant ribosome profiles in Aspergillus nidulans
Molecular microbiology, 2023
Bharudin, I., Caddick, M.X., Connell, S.R., Lamaudière, M.T. and Morozov, I.Y.
The mRNA decapping mechanism, which involves the Dcp1-Dcp2 complex, plays a crucial role in RNA degradation in eukaryote, one of which is nonsense-mediated decay (NMD). NMD is a mechanism that identifies and suppresses abnormal RNA transcripts containing premature termination codons, leading to their rapid degradation.
This study investigates NMD in Aspergillus nidulans, whereby the authors generated mutant strains to disrupt decapping factors and analyzed the ribosomal profiles by sucrose gradient analysis. In the Δdcp1 strain, an abnormal ribosomal profile was observed, with the accumulation of a distinct ribosomal band containing specific rRNA fragments. By identifying rRNA cleavage sites, it was demonstrated that Dcp2, the catalytic component of the decapping complex, may be directly involved in mediating these cleavage events in the absence of Dcp1. The aberrant ribosomal profile observed in the Δdcp1 strain indicates a potential role of decapping factors in ribosomal RNA cleavage and turnover. The accumulation of partially degraded, non-functional ribosomal RNA may lead to reduced translation and disrupted ribosome recycling.
In summary, it was shown that decapping factors and the principal exonuclease Xrn1 are not required for NMD in this organism, unlike in Saccharomyces cerevisiae. This suggests that A. nidulans may have additional mechanisms that bypass the need for decapping in NMD. The study highlights that the requirement for decapping in nonsense-mediated decay (NMD) can vary among different organisms. Further investigation is needed to understand the precise mechanisms and consequences of these findings, including the involvement of the Dcp2 catalytic domain in ribosomal RNA cleavage and the relationship between ribosomal fragmentation and translation efficiency in A. nidulans.
